diff --git a/envs/genomescope.yaml b/envs/genomescope.yaml
new file mode 100644
index 0000000000000000000000000000000000000000..e852490bd58cb8416bfeb7ca9dda514b3221d14e
--- /dev/null
+++ b/envs/genomescope.yaml
@@ -0,0 +1,6 @@
+channels:
+  - bioconda
+  - conda-forge
+dependencies:
+  - genomescope2=2.0
+  - python=3.9.2
diff --git a/envs/merylMerq.yaml b/envs/merylMerq.yaml
index a7d2a4e35e66b8fe7b04a37d6ea44a2bf16ae128..96c6aedf8e1ed57389eff28c2921f46dab7d18db 100644
--- a/envs/merylMerq.yaml
+++ b/envs/merylMerq.yaml
@@ -1,15 +1,12 @@
 channels:
-  - bioconda
   - conda-forge
-  - r
+  - bioconda
 dependencies:
   - igvtools
   - openjdk=11.0.8
-  - r=3
+  - r-base=3.6.3
   - r-ggplot2
   - r-argparse
   - r-scales
-  - genomescope2=2.0
   - samtools
   - bedtools
-  - python=3.9.2
diff --git a/programs/merqury-1.1/LICENSE b/programs/merqury-1.1/LICENSE
new file mode 100644
index 0000000000000000000000000000000000000000..16968438d07f14775ea0b351619498049614976f
--- /dev/null
+++ b/programs/merqury-1.1/LICENSE
@@ -0,0 +1,19 @@
+
+  PUBLIC DOMAIN NOTICE
+
+  This software is "United States Government Work" under the terms of the United
+  States Copyright Act. It was written as part of the authors' official duties
+  for the United States Government and thus cannot be copyrighted. This software
+  is freely available to the public for use without a copyright
+  notice. Restrictions cannot be placed on its present or future use.
+
+  Although all reasonable efforts have been taken to ensure the accuracy and
+  reliability of the software and associated data, the National Human Genome
+  Research Institute (NHGRI), National Institutes of Health (NIH) and the
+  U.S. Government do not and cannot warrant the performance or results that may
+  be obtained by using this software or data. NHGRI, NIH and the U.S. Government
+  disclaim all warranties as to performance, merchantability or fitness for any
+  particular purpose.
+
+  Please cite the authors in any work or product based on this material.
+
diff --git a/programs/merqury-1.1/README.md b/programs/merqury-1.1/README.md
new file mode 100644
index 0000000000000000000000000000000000000000..4808a8cd8913408800e2289804e93c05b9b81d17
--- /dev/null
+++ b/programs/merqury-1.1/README.md
@@ -0,0 +1,191 @@
+# Merqury
+
+## Evaluate genome assemblies with k-mers and more
+
+Often, genome assembly projects have illumina whole genome sequencing reads available for the assembled individual.
+The k-mer spectrum of this read set can be used for independently evaluating assembly quality without the need of a high quality reference.
+Merqury provides a set of tools for this purpose.
+
+## Dependency
+* gcc 4.8 or higher
+* meryl
+* Java run time environment (JRE)
+* R with argparse, ggplot2, and scales (tested on R 3.6.1)
+* bedtools
+* samtools
+* igvtools
+
+## Installation
+
+### Get a working meryl in your PATH
+Download meryl release: https://github.com/marbl/meryl/releases/tag/v1.0
+
+If the binary doesn't work, download the source and compile:
+```shell
+cd meryl/src
+make -j 24
+export PATH=/path/to/meryl/…/bin:$PATH
+```
+See if we get help message for `meryl`.
+
+### Add a path variable MERQURY
+```shell
+git clone https://github.com/marbl/merqury.git
+cd merqury
+export MERQURY=$PWD
+```
+Add the “export” part to your environment (~/.bash_profile or ~/.profile).
+Add installation dir paths for `bedtools`, `samtools` and `igvtools` to your enviroenment.
+`source` it.
+
+
+## Run
+
+* !! Merqury assumes all meryl dbs (dirs) are named with `.meryl`. !!
+
+On a single machine:
+```
+ln -s $MERQURY/merqury.sh		# Link merqury
+./merqury.sh <read-db.meryl> [<mat.meryl> <pat.meryl>] <asm1.fasta> [asm2.fasta] <out>
+
+Usage: merqury.sh <read-db.meryl> [<mat.meryl> <pat.meryl>] <asm1.fasta> [asm2.fasta] <out>
+	<read-db.meryl>	: k-mer counts of the read set
+	<mat.meryl>		: k-mer counts of the maternal haplotype (ex. mat.only.meryl or mat.hapmer.meryl)
+	<pat.meryl>		: k-mer counts of the paternal haplotype (ex. pat.only.meryl or pat.hapmer.meryl)
+	<asm1.fasta>	: Assembly fasta file (ex. pri.fasta, hap1.fasta or maternal.fasta)
+	[asm2.fasta]	: Additional fasta file (ex. alt.fasta, hap2.fasta or paternal.fasta)
+	*asm1.meryl and asm2.meryl will be generated. Avoid using the same names as the hap-mer dbs
+	<out>		: Output prefix
+```
+`< >` : required  
+`[ ]` : optional
+
+## Example
+
+Below is showing examples how to run Merqury using the prebuilt meryl dbs on a. thaliana F1 hybrid.
+The fasta files are the trio-binned assemblies from [Koren et al](https://doi.org/10.1038/nbt.4277).
+
+```shell
+### Download assemblies ###
+wget https://gembox.cbcb.umd.edu/triobinning/athal_COL.fasta
+wget https://gembox.cbcb.umd.edu/triobinning/athal_CVI.fasta
+
+### Download prebuilt meryl dbs ###
+# read.meryl of the F1 hybrid between COL-0 and CVI-0
+wget https://obj.umiacs.umd.edu/marbl_publications/merqury/athal/a_thal.k18.meryl.tar.gz
+# hap-mers for COL-0 haplotype
+wget https://obj.umiacs.umd.edu/marbl_publications/merqury/athal/a_thal.col0.hapmer.meryl.tar.gz
+# hap-mers for CVI-0 haplotype
+wget https://obj.umiacs.umd.edu/marbl_publications/merqury/athal/a_thal.cvi0.hapmer.meryl.tar.gz
+
+# Untar
+for gz in *.tar.gz
+do
+    tar -zxf $gz
+done
+
+# Run merqury
+$MERQURY/merqury.sh F1.k18.meryl col0.hapmer.meryl cvi0.hapmer.meryl athal_COL.fasta athal_CVI.fasta test
+```
+
+
+### 1. I have one assembly (pseudo-haplotype or mixed-haplotype)
+```shell
+# I don't have the hap-mers
+$MERQURY/merqury.sh read-db.meryl asm1.fasta out_prefix
+# Using the example above
+$MERQURY/merqury.sh F1.k18.meryl athal_COL.fasta test-1
+
+# I have the hap-mers
+$MERQURY/merqury.sh read-db.meryl mat.meryl pat.meryl asm1.fasta out_prefix
+# Using the example above
+$MERQURY/merqury.sh F1.k18.meryl col0.hapmer.meryl cvi0.hapmer.meryl athal_COL.fasta test-1
+```
+
+### 2. I have two assemblies (diploid)
+```shell
+# I don't have the hap-mers
+$MERQURY/merqury.sh read-db.meryl asm1.fasta asm2.fasta out_prefix
+# Using the example above
+$MERQURY/merqury.sh F1.k18.meryl athal_COL.fasta athal_CVI.fasta test-2
+
+# I have the hap-mers
+$MERQURY/merqury.sh read-db.meryl mat.meryl pat.meryl asm1.fasta asm2.fasta out_prefix
+# Using the example above
+$MERQURY/merqury.sh F1.k18.meryl col0.hapmer.meryl cvi0.hapmer.meryl athal_COL.fasta athal_CVI.fasta test-2
+```
+
+* Note there is no need to run merqury per-assemblies. Give two fasta files, Merqury generates stats for each and combined.
+
+
+
+### How to parallelize
+Merqury starts with `eval/spectra_cn.sh`.
+When hap-mers are provided, merqury runs modules under `trio/` in addition to `eval/spectra_cn.sh`.
+
+
+The following can run at the same time. Modules with dependency are followed by arrows (->).
+* `eval/spectra_cn.sh` -> `trio/spectra_hap.sh`
+* `trio/hap_blob.sh`
+* `trio/phase_block.sh` per assembly -> `trio/block_n_stats.sh`
+
+
+Meryl, the k-mer counter inside, uses the maximum cpus available.
+Set `OMP_NUM_THREADS=24` for example to use 24 threads.
+
+On slurm environment, simply run:
+```
+ln -s $MERQURY/_submit_merqury.sh	# Link merqury
+./_submit_merqury.sh <read-db.meryl> [<mat.meryl> <pat.meryl>] <asm1.fasta> [asm2.fasta] <out>
+```
+Change the `sbatch` to match your environment. (ex. partition)
+
+
+## Outputs from each modules
+* `eval/spectra_cn.sh`: k-mer completeness, qv, spectra-cn and spectra-asm plots, asm-only `.bed` and `.tdf` for tracking errors
+* `eval/qv.sh`: just get the qv stats and quit.
+* `trio/spectra_hap.sh`: hap-mer level spectra-cn plots, hap-mer completeness
+* `trio/hap_blob.sh`: blob plots of the hap-mers in each contg/scaffold
+* `trio/phase_block.sh`: phase block statistics, phase block N* plots, hap-mer tracks (`.bed` and `.tdf` files)
+* `trio/block_n_stats.sh`: continuity plots (phase block N* or NG* plots, phase block vs. contig/scaffold plots)
+* `trio/switch_error.sh`: this is run part of `phase_blck.sh`, however can be re-run with desired short-range switch parameters. Run `trio/block_n_stats.sh` along with it to get the associated plots.
+
+## Tips for helps
+Run each script without any parameters if not sure what to do.
+For example, `./trio/switch_error.sh` will give a help message and quit.
+
+Following wiki pages have more detailed examples.
+
+## 1. Prepare meryl dbs ([details](https://github.com/marbl/merqury/wiki/1.-Prepare-meryl-dbs))
+1. Get the right k size
+2. Build k-mer dbs with meryl
+3. Build hap-mers for trios
+
+## 2. Overall assembly evaluation ([details](https://github.com/marbl/merqury/wiki/2.-Overall-k-mer-evaluation))
+1. Reference free QV estimate
+2. k-mer completeness (recovery rate)
+3. Spectra copy number analysis
+4. Track error bases in the assembly
+
+## 3. Phasing assessment with hap-mers ([details](https://github.com/marbl/merqury/wiki/3.-Phasing-assessment-with-hap-mers))
+1. Inherited hap-mer plots
+2. Hap-mer blob plots
+3. Hap-mer completeness (recovery rate)
+4. Spectra copy number analysis per hap-mers
+5. Phased block statistics and switch error rates
+6. Track each haplotype block in the assembly
+
+## Available pre-built meryl dbs
+Meryl dbs from Illumina WGS and hapmers are available [here](https://obj.umiacs.umd.edu/marbl_publications/merqury/index.html) for
+* A. thaliana COL-0 x CVI-0 F1
+* NA12878 (HG001)
+* HG002
+
+## Citing merqury
+
+Please use the following [preprint](https://www.biorxiv.org/content/10.1101/2020.03.15.992941v1) to cite Merqury:
+
+Arang Rhie, Brian P. Walenz, Sergey Koren, Adam M. Phillippy, Merqury: reference-free quality and phasing assessment for genome assemblies, bioRxiv (2020). doi: https://doi.org/10.1101/2020.03.15.992941
+
+
+
diff --git a/programs/merqury_June2020/_submit_build.sh b/programs/merqury-1.1/_submit_build.sh
similarity index 96%
rename from programs/merqury_June2020/_submit_build.sh
rename to programs/merqury-1.1/_submit_build.sh
index 988e26d1fd5c56f7f5ef73c2d03f4e5cc4a9adce..e44a8b8a7adc2bc162afdf19ce86f9d9af6a0ad0 100755
--- a/programs/merqury_June2020/_submit_build.sh
+++ b/programs/merqury-1.1/_submit_build.sh
@@ -45,11 +45,11 @@ for i in $(seq 1 $LEN)
 do
 	fq=`sed -n ${i}p $input_fofn`
 	GB=`du -k $fq  | awk '{printf "%.0f", $1/1024/1024}'`
-	if [[ $GB -lt 12 ]]; then
-	    echo "$fq is $GB, less than 12GB. Skip splitting."
+	if [[ $GB -lt 15 ]]; then
+	    echo "$fq is $GB, less than 15GB. Skip splitting."
 	    echo $fq >> $input_fofn.$i
 	else
-	    echo "$fq is $GB, over 12GB. Will split and run meryl in parallel."
+	    echo "$fq is $GB, over 15GB. Will split and run meryl in parallel."
 	    echo "Split files will be in $input_fofn.$i"
 	    args="$input_fofn"
 	    split_arrs="$split_arrs$i,"
diff --git a/programs/merqury_June2020/_submit_build_10x.sh b/programs/merqury-1.1/_submit_build_10x.sh
similarity index 98%
rename from programs/merqury_June2020/_submit_build_10x.sh
rename to programs/merqury-1.1/_submit_build_10x.sh
index 6c424db5743253a9cf70ba5c334cc9958869f58c..c1c9c4292d5da41e4ecbff188b511ce01e0057dd 100755
--- a/programs/merqury_June2020/_submit_build_10x.sh
+++ b/programs/merqury-1.1/_submit_build_10x.sh
@@ -1,6 +1,6 @@
 #!/bin/bash
 
-build=/srv/public/users/tomas/programs/merqury/build
+build=$MERQURY/build
 
 if [ -z $1 ]; then
     echo "Usage: ./_submit_build.sh <k-size> <R1.fofn> <R2.fofn> <out_prefix> [mem=T]"
diff --git a/programs/merqury_June2020/_submit_hapmers.sh b/programs/merqury-1.1/_submit_hapmers.sh
similarity index 100%
rename from programs/merqury_June2020/_submit_hapmers.sh
rename to programs/merqury-1.1/_submit_hapmers.sh
diff --git a/programs/merqury_June2020/_submit_merqury.sh b/programs/merqury-1.1/_submit_merqury.sh
similarity index 100%
rename from programs/merqury_June2020/_submit_merqury.sh
rename to programs/merqury-1.1/_submit_merqury.sh
diff --git a/programs/merqury_June2020/_submit_split.sh b/programs/merqury-1.1/_submit_split.sh
similarity index 100%
rename from programs/merqury_June2020/_submit_split.sh
rename to programs/merqury-1.1/_submit_split.sh
diff --git a/programs/merqury_June2020/best_k.sh b/programs/merqury-1.1/best_k.sh
similarity index 100%
rename from programs/merqury_June2020/best_k.sh
rename to programs/merqury-1.1/best_k.sh
diff --git a/programs/merqury_June2020/build/concat_splits.sh b/programs/merqury-1.1/build/concat_splits.sh
similarity index 100%
rename from programs/merqury_June2020/build/concat_splits.sh
rename to programs/merqury-1.1/build/concat_splits.sh
diff --git a/programs/merqury_June2020/build/count.sh b/programs/merqury-1.1/build/count.sh
similarity index 100%
rename from programs/merqury_June2020/build/count.sh
rename to programs/merqury-1.1/build/count.sh
diff --git a/programs/merqury_June2020/build/count_10x.sh b/programs/merqury-1.1/build/count_10x.sh
similarity index 74%
rename from programs/merqury_June2020/build/count_10x.sh
rename to programs/merqury-1.1/build/count_10x.sh
index 8ec5736d1ae44092fde0f7ea669c1032c78165b0..1f5e22600379bbc9a0933bda7ec6deafb9ebc8c0 100755
--- a/programs/merqury_June2020/build/count_10x.sh
+++ b/programs/merqury-1.1/build/count_10x.sh
@@ -28,9 +28,19 @@ else
     line_num=$SLURM_ARRAY_TASK_ID
 fi
 
-#  Note: Provide memory in Gb unit. SLURM provides $SLURM_MEM_PER_NODE in Mb.
-#            Give extra 4Gb to avoid 'Bus Error' form running out of memory.
-mem=$(((SLURM_MEM_PER_NODE/1024)-4))
+if [[ ! -z $SLURM_CPUS_PER_TASK ]]; then
+	cpus="threads=$SLURM_CPUS_PER_TASK"
+fi
+
+# If SLURM_MEM_PER_NODE exist; give extra 4Gb
+# otherwise, let meryl determine
+if [[ ! -z $SLURM_MEM_PER_NODE ]]; then
+	# Note: Provide memory in Gb unit. SLURM provides $SLURM_MEM_PER_NODE in Mb.
+	# Give extra 4Gb to avoid 'Bus Error' form running out of memory.
+	mem=$(((SLURM_MEM_PER_NODE/1024)-4))
+	mem="memory=$mem"
+fi
+
 line_num=$(((offset * 1000) + $line_num))
 
 # Read in the input path
@@ -45,9 +55,9 @@ output=$name.$k.$line_num.meryl
 if [ ! -d $output ]; then
     # Run meryl count: Collect k-mer frequencies
     echo "
-    zcat $input | awk '{if (NR%2==1) {print $1} else {print substr($1,24)}}' | meryl k=$k threads=$SLURM_CPUS_PER_TASK memory=$mem count output $output -
+    zcat $input | awk '{if (NR%2==1) {print $1} else {print substr($1,24)}}' | meryl k=$k $cpus $mem count output $output -
     "
-    zcat $input | awk '{if (NR%2==1) {print $1} else {print substr($1,24)}}' | meryl k=$k threads=$SLURM_CPUS_PER_TASK memory=$mem count output $output -
+    zcat $input | awk '{if (NR%2==1) {print $1} else {print substr($1,24)}}' | meryl k=$k $cpus $mem count output $output -
 else
     echo "$output dir already exist. Nothing to do with $name."
 fi
diff --git a/programs/merqury_June2020/build/diff.sh b/programs/merqury-1.1/build/diff.sh
similarity index 100%
rename from programs/merqury_June2020/build/diff.sh
rename to programs/merqury-1.1/build/diff.sh
diff --git a/programs/merqury_June2020/build/filt.sh b/programs/merqury-1.1/build/filt.sh
similarity index 100%
rename from programs/merqury_June2020/build/filt.sh
rename to programs/merqury-1.1/build/filt.sh
diff --git a/programs/merqury_June2020/build/intersect.sh b/programs/merqury-1.1/build/intersect.sh
similarity index 100%
rename from programs/merqury_June2020/build/intersect.sh
rename to programs/merqury-1.1/build/intersect.sh
diff --git a/programs/merqury_June2020/build/split.sh b/programs/merqury-1.1/build/split.sh
similarity index 91%
rename from programs/merqury_June2020/build/split.sh
rename to programs/merqury-1.1/build/split.sh
index 40e3980adb39b67da87c8dfcc4385674e9893c49..9dca1508bd7a60b1115966a4a4d4a2ca618683bd 100755
--- a/programs/merqury_June2020/build/split.sh
+++ b/programs/merqury-1.1/build/split.sh
@@ -3,7 +3,7 @@
 echo "Usage: ./split.sh <input.fofn> [LINE_NUM]"
 echo -e "\t<input.fofn>: fastq.gz files we want to split by every 300 million lines."
 echo -e "\t<input.fofn>.LINE_NUM will be generated."
-echo -e "\t\tUse it for building meryl dbs"
+echo -e "\t\tUse it for building meryl dbs. pigz will use maximum of 8 processes by default."
 echo
 
 FOFN=$1
@@ -25,6 +25,9 @@ if [ -z $tid ]; then
 fi
 
 cpus=$SLURM_CPUS_PER_TASK
+if [[ -z $cpus ]]; then
+    cpus=8
+fi
 
 fq=`sed -n ${tid}p $FOFN`
 fq_prefix=`echo $fq | sed 's/.fastq.gz$//g' | sed 's/.fq.gz$//g' | sed 's/.fastq$//g' | sed 's/.fq$//g'`
diff --git a/programs/merqury_June2020/build/split_10x.sh b/programs/merqury-1.1/build/split_10x.sh
similarity index 87%
rename from programs/merqury_June2020/build/split_10x.sh
rename to programs/merqury-1.1/build/split_10x.sh
index 66540966f62f5f5e1fcaeb50a97b0c240de266ba..e1252338a0cee3eb01259d64284a655858ccbc12 100755
--- a/programs/merqury_June2020/build/split_10x.sh
+++ b/programs/merqury-1.1/build/split_10x.sh
@@ -3,7 +3,7 @@
 echo "Usage: ./split_10x.sh <input.fofn> [LINE_NUM]"
 echo -e "\t<input.fofn>: 10XG fastq R1.gz files to split per 300 million lines."
 echo -e "\t<input.fofn>.LINE_NUM will be generated."
-echo -e "\t\tUse it for building meryl dbs"
+echo -e "\t\tUse it for building meryl dbs. pigz will use maximum of 8 processes by default."
 echo
 
 FOFN=$1
@@ -12,7 +12,7 @@ if [ -z $FOFN ]; then
     exit -1
 fi
 
-tid=300000000	# slurm environment variable for job arrays
+tid=$SLURM_ARRAY_TASK_ID	# slurm environment variable for job arrays
 LINE_NUM=$2
 
 if [ -z $tid ]; then
@@ -24,11 +24,13 @@ if [ -z $tid ]; then
     exit -1
 fi
 
-cpus=20
+cpus=$SLURM_CPUS_PER_TASK
+if [[ -z $cpus ]]; then
+    cpus=8
+fi
 
 fq=`sed -n ${tid}p $FOFN`
 fq_prefix=`echo $fq | sed 's/.fastq.gz$//g' | sed 's/.fq.gz$//g' | sed 's/.fastq$//g' | sed 's/.fq$//g'`
-echo $fq_prefix
 fq_prefix=`basename $fq_prefix`
 
 mkdir -p split
diff --git a/programs/merqury_June2020/build/union_sum.sh b/programs/merqury-1.1/build/union_sum.sh
similarity index 90%
rename from programs/merqury_June2020/build/union_sum.sh
rename to programs/merqury-1.1/build/union_sum.sh
index dc21905b1a01f117df1762d83a368fd6fd1b0247..a01c15e7f0c0cc35efb2e211e4c8080982e2ec6a 100755
--- a/programs/merqury_June2020/build/union_sum.sh
+++ b/programs/merqury-1.1/build/union_sum.sh
@@ -16,8 +16,6 @@ output_prefix=$3.k$k
 LEN=`wc -l $input_fofn | awk '{print $1}'`
 NUM_DBS_TO_JOIN=100	# Join every $NUM_DBS_TO_JOIN as intermediates, then merge at the end
 JOIN_IDX=0
-CPU=$SLURM_CPUS_PER_TASK
-MEM=$SLURM_MEM_PER_NODE
 
 echo "Set ulimit: ulimit -Sn 32000"
 ulimit -Sn 32000
@@ -44,8 +42,6 @@ do
 	if [ ! -d $output ]; then
 	    echo "
 	    meryl \
-	        threads=$CPU \
-	        memory=$((MEM/1024)) \
 	        k=$k \
 	        union-sum \
 	        output $output \
@@ -53,8 +49,6 @@ do
 	    "
 
 	    meryl \
-	        threads=$CPU \
-	        memory=$((MEM/1024)) \
 	        k=$k \
 	        union-sum \
 	        output $output \
@@ -97,8 +91,6 @@ echo "union-sum of $output_prefix.[ 1 - $JOIN_IDX ] :"
 if [ ! -d $output_prefix ]; then
     echo "
     meryl \
-        threads=$CPU \
-        memory=$((MEM/1024)) \
         k=$k \
         union-sum \
         output $output_prefix.meryl \
@@ -106,8 +98,6 @@ if [ ! -d $output_prefix ]; then
     "
 
     meryl \
-        threads=$CPU \
-        memory=$((MEM/1024)) \
         k=$k \
         union-sum \
         output $output_prefix.meryl \
diff --git a/programs/merqury-1.1/eval/asm_multiplicity.sh b/programs/merqury-1.1/eval/asm_multiplicity.sh
new file mode 100755
index 0000000000000000000000000000000000000000..51ed3ec40a9acd672d999004dfc8b4abdf373bd7
--- /dev/null
+++ b/programs/merqury-1.1/eval/asm_multiplicity.sh
@@ -0,0 +1,33 @@
+#!/bin/sh
+
+if [[ "$#" -lt 3 ]]; then
+	echo "Usage: ./asm_multiplicity.sh <asm.fasta> <asm.meryl> <out>"
+	echo -e "\t<asm.fasta>: assembly fasta file"
+	echo -e "\t<asm.meryl>: assembly meryl dir"
+	echo -e "\t<out>: output file prefix. <out>.copies.wig and <out>.asm_multiplicity.bigWig will be generated."
+	exit 0
+fi
+
+asm_fa=$1
+asm=$2
+out=$3
+
+# Requirements: samtools, ucsc kent utils
+module load samtools
+module load ucsc/396
+
+if [[ ! -e $asm_fa ]]; then
+	samtools faidx $asm_fa
+fi
+
+
+echo "
+# Collect copy numbers in assembly"
+meryl-lookup -dump -memory 12 -sequence $asm_fa -mers $asm | awk '$4=="T"' | java -jar -Xmx1g $MERQURY/util/merylDumpToWig.jar - > $out.copies.wig
+
+echo "
+# Convert to bigwig"
+wigToBigWig $out.copies.wig $asm_fa.fai $out.asm_multiplicity.bigWig
+
+echo "Done!"
+
diff --git a/programs/merqury_June2020/eval/bedCalcN50.jar b/programs/merqury-1.1/eval/bedCalcN50.jar
similarity index 100%
rename from programs/merqury_June2020/eval/bedCalcN50.jar
rename to programs/merqury-1.1/eval/bedCalcN50.jar
diff --git a/programs/merqury-1.1/eval/false_duplications.sh b/programs/merqury-1.1/eval/false_duplications.sh
new file mode 100755
index 0000000000000000000000000000000000000000..ed7bf0a61ccccd3c18dffb3a7589a518d4a3fcff
--- /dev/null
+++ b/programs/merqury-1.1/eval/false_duplications.sh
@@ -0,0 +1,21 @@
+#!/bin/bash
+
+if [[ -z $1 ]]; then
+	echo "Usage: ./false_duplications.sh <name.asm.spectra-cn.hist>"
+	echo "Get the number of additional k-mers found in an assembly in the single and two copy k-mer peaks from the reads"
+	echo -e "<name.asm.spectra-cn.hist>: spectra-cn.hist generated with Merqury for a pseudo-haplotype or mixed haplotype assembly"
+	exit 0
+fi
+
+hist=$1
+
+cutoff=`cat $hist  | awk '$1==1 {print $2"\t"$3}' | awk -v max=0 'max<$2 {max=$2; mult=$1 } END {printf "%.0f\n", mult*(1.5)}'`
+one_cp=`awk -v cutoff=$cutoff '$1==1 && $2<cutoff {sum+=$NF} END {print sum}' $hist`
+two_cp=`awk -v cutoff=$cutoff '$1==2 && $2<cutoff {sum+=$NF} END {print sum}' $hist`
+thr_cp=`awk -v cutoff=$cutoff '$1==3 && $2<cutoff {sum+=$NF} END {print sum}' $hist`
+fou_cp=`awk -v cutoff=$cutoff '$1==4 && $2<cutoff {sum+=$NF} END {print sum}' $hist`
+mor_cp=`awk -v cutoff=$cutoff '$1==">4" && $2<cutoff {sum+=$NF} END {print sum}' $hist`
+DUPS_TOTAL=`echo "$one_cp $two_cp $thr_cp $fou_cp $mor_cp" | awk '{dup=$2+$3+$4+$5; all=dup+$1} END {print $1"\t"$2"\t"$3"\t"$4"\t"$5"\t"dup"\t"all"\t"(100*dup/all)}'`
+echo -e "hist\tcutoff\t1\t2\t3\t4\t>4\tdup(>1)\tall\tdup%"
+echo -e "$hist\t$cutoff\t$DUPS_TOTAL"
+
diff --git a/programs/merqury_June2020/eval/kmerHistToPloidyDepth.jar b/programs/merqury-1.1/eval/kmerHistToPloidyDepth.jar
similarity index 100%
rename from programs/merqury_June2020/eval/kmerHistToPloidyDepth.jar
rename to programs/merqury-1.1/eval/kmerHistToPloidyDepth.jar
diff --git a/programs/merqury-1.1/eval/per_seq_qv.sh b/programs/merqury-1.1/eval/per_seq_qv.sh
new file mode 100755
index 0000000000000000000000000000000000000000..9f0125d97f54117759025ac68665318915c4184d
--- /dev/null
+++ b/programs/merqury-1.1/eval/per_seq_qv.sh
@@ -0,0 +1,43 @@
+#!/bin/sh
+
+if [[ "$#" -lt 3 ]]; then
+	echo "Usage: ./per_seq_qv.sh seq.fasta read.meryl out"
+	echo ""
+	echo "Get QV per seqIDs in seq.fasta"
+	echo -e "seq.fasta:\tassembly, multi-fasta file"
+	echo -e "read.meryl:\tk-mer counts of read set"
+	echo -e "out:\toutput prefix"
+	echo
+	echo "Output will be generated as out.qv"
+	echo "Arang Rhie, 2020-06-15. arrhie@gmail.com"
+	echo
+	exit 0
+fi
+
+seq=$1	# asm.fasta
+read=$2	# read.meryl
+name=$3	# output prefix
+
+k=`meryl print $read | head -n 2 | tail -n 1 | awk '{print length($1)}'`
+echo "Detected k-mer size $k"
+echo
+
+seq_name=`echo $seq | sed 's/.fasta$//g' | sed 's/.fa$//g'`
+
+
+if [[ ! -e $seq_name.0.meryl ]]; then
+
+	if [[ ! -e $seq_name.meryl ]]; then
+		echo "# No $seq_name.meryl found. Counting ${k}-mers..."
+		meryl count k=$k output $seq_name.meryl $seq
+		echo
+	fi
+	echo "# Collect k-mers found in $seq_name only"
+	meryl difference $seq_name.meryl $read output $seq_name.0.meryl
+	echo
+fi
+
+echo "QV per sequences"
+meryl-lookup -existence -sequence $seq -mers $seq_name.0.meryl/ | \
+   awk -v k=$k '{print $1"\t"$NF"\t"$(NF-2)"\t"(-10*log(1-(1-$NF/$(NF-2))^(1/k))/log(10))"\t"(1-(1-$NF/$(NF-2))^(1/k))}' > $name.qv
+
diff --git a/programs/merqury_June2020/eval/qv.sh b/programs/merqury-1.1/eval/qv.sh
similarity index 87%
rename from programs/merqury_June2020/eval/qv.sh
rename to programs/merqury-1.1/eval/qv.sh
index bc37f0087ea154459c2ff3061ffeb846e0c31668..c5ccdaff463506834ffa5b008920dd92ea693965 100755
--- a/programs/merqury_June2020/eval/qv.sh
+++ b/programs/merqury-1.1/eval/qv.sh
@@ -50,6 +50,9 @@ do
         QV=`echo "$ASM_ONLY $TOTAL" | awk -v k=$k '{print (-10*log(1-(1-$1/$2)^(1/k))/log(10))}'`
         echo -e "$asm\t$ASM_ONLY\t$TOTAL\t$QV\t$ERROR" >> $name.qv
         echo
+
+        meryl-lookup -existence -sequence $asm_fa -mers $asm.0.meryl/ | \
+        awk -v k=$k '{print $1"\t"$NF"\t"$(NF-2)"\t"(-10*log(1-(1-$NF/$(NF-2))^(1/k))/log(10))"\t"(1-(1-$NF/$(NF-2))^(1/k))}' > $name.$asm.qv
 done
 
 if [[ "$asm2_fa" == "" ]]; then
@@ -62,8 +65,8 @@ asm2=`echo $asm2_fa | sed 's/.fasta.gz//g' | sed 's/.fa.gz//g' | sed 's/.fasta//
 
 asm="both"
 
-meryl union output $asm.meryl   $asm1.meryl   $asm2.meryl
-meryl union output $asm.0.meryl $asm1.0.meryl $asm2.0.meryl
+meryl union-sum output $asm.meryl   $asm1.meryl   $asm2.meryl
+meryl union-sum output $asm.0.meryl $asm1.0.meryl $asm2.0.meryl
 
 echo "# QV statistics for $asm"
 ASM_ONLY=`meryl statistics $asm.0.meryl  | head -n4 | tail -n1 | awk '{print $2}'`
@@ -75,3 +78,4 @@ echo
 
 rm -r $asm1.0.meryl $asm1.meryl $asm2.0.meryl $asm2.meryl $asm.0.meryl $asm.meryl
 echo "Done!"
+
diff --git a/programs/merqury-1.1/eval/read_multiplicity.sh b/programs/merqury-1.1/eval/read_multiplicity.sh
new file mode 100755
index 0000000000000000000000000000000000000000..062add8a8e4179a66c91cef4cc79863311ab175d
--- /dev/null
+++ b/programs/merqury-1.1/eval/read_multiplicity.sh
@@ -0,0 +1,31 @@
+#!/bin/sh
+
+if [[ "$#" -lt 3 ]]; then
+	echo "Usage: ./read_multiplicity.sh <asm.fasta> <read.meryl> <out>"
+	echo -e "\t<asm.fasta>: assembly fasta file"
+	echo -e "\t<read.meryl>: k-mer counts of the reads"
+	echo -e "\t<out>: output file prefix. <out>.read.wig and <out>.read_multiplicity.bigWig will be generated."
+	exit 0
+fi
+
+asm_fa=$1
+read=$2
+out=$3
+asm=`echo $asm_fa | sed 's/.gz$//g' | sed 's/.fasta$//g' | sed 's/.fa$//g'`
+
+module load samtools
+module load ucsc/396
+
+if [[ ! -e $asm_fa.fai ]]; then
+	samtools faidx $asm_fa
+fi
+
+echo "
+# Collect k-mer multiplicity in reads"
+# Adjust memory accordingly
+meryl-lookup -dump -memory 68 -sequence $asm_fa -mers $read | awk '$4=="T"' | java -jar -Xmx1g $MERQURY/util/merylDumpToWig.jar - > $out.read.wig
+
+echo "
+# Convert to bigwig"
+wigToBigWig $out.read.wig $asm_fa.fai $out.read_multiplicity.bigwig
+
diff --git a/programs/merqury_June2020/eval/spectra-cn.sh b/programs/merqury-1.1/eval/spectra-cn.sh
similarity index 92%
rename from programs/merqury_June2020/eval/spectra-cn.sh
rename to programs/merqury-1.1/eval/spectra-cn.sh
index 03386999291257d2096a7d6737324d21392e2acb..f528c474c5f410e85e817e8dffe8f1596aa329c0 100755
--- a/programs/merqury_June2020/eval/spectra-cn.sh
+++ b/programs/merqury-1.1/eval/spectra-cn.sh
@@ -115,8 +115,8 @@ do
 
 	echo "# Plot $hist"
 	echo "\
-	$MERQURY/plot/plot_spectra_cn.R -f $hist -o $name.spectra-cn -z $hist_asm_only"
-	$MERQURY/plot/plot_spectra_cn.R -f $hist -o $name.spectra-cn -z $hist_asm_only
+	Rscript $MERQURY/plot/plot_spectra_cn.R -f $hist -o $name.$asm.spectra-cn -z $hist_asm_only"
+	Rscript $MERQURY/plot/plot_spectra_cn.R -f $hist -o $name.$asm.spectra-cn -z $hist_asm_only
 	echo
 
 	echo "# QV statistics"
@@ -127,6 +127,11 @@ do
         echo -e "$asm\t$ASM_ONLY\t$TOTAL\t$QV\t$ERROR" >> $name.qv
 	echo
 
+	echo "# Per seq QV statistics"
+	meryl-lookup -existence -sequence $asm_fa -mers $asm.0.meryl/ | \
+	awk -v k=$k '{print $1"\t"$NF"\t"$(NF-2)"\t"(-10*log(1-(1-$NF/$(NF-2))^(1/k))/log(10))"\t"(1-(1-$NF/$(NF-2))^(1/k))}' > $name.$asm.qv
+	echo
+
         echo "# k-mer completeness (recoveray rate) with solid k-mers for $asm with > $filt counts"
 	meryl intersect output $asm.solid.meryl $asm.meryl $read_solid
         TOTAL=`meryl statistics $read_solid | head -n3 | tail -n1 | awk '{print $2}'`
@@ -177,8 +182,8 @@ if [[ "$asm2_fa" = "" ]]; then
 
 	echo "#	Plot $hist"
 	echo "\
-	$MERQURY/plot/plot_spectra_cn.R -f $hist -o $name.spectra-asm -z $hist_asm_dist_only"
-	$MERQURY/plot/plot_spectra_cn.R -f $hist -o $name.spectra-asm -z $hist_asm_dist_only
+	Rscript $MERQURY/plot/plot_spectra_cn.R -f $hist -o $name.spectra-asm -z $hist_asm_dist_only"
+	Rscript $MERQURY/plot/plot_spectra_cn.R -f $hist -o $name.spectra-asm -z $hist_asm_dist_only
 	echo
 
 	echo "# Clean up"
@@ -265,8 +270,8 @@ echo
 
 echo "# Plot $hist"
 echo "\
-$MERQURY/plot/plot_spectra_cn.R -f $hist -o $name.spectra-cn -z $hist_asm_only"
-$MERQURY/plot/plot_spectra_cn.R -f $hist -o $name.spectra-cn -z $hist_asm_only
+Rscript $MERQURY/plot/plot_spectra_cn.R -f $hist -o $name.spectra-cn -z $hist_asm_only"
+Rscript $MERQURY/plot/plot_spectra_cn.R -f $hist -o $name.spectra-cn -z $hist_asm_only
 echo
 
 echo "# QV"
@@ -317,7 +322,7 @@ else
 fi
 
 echo "Plot $hist"
-$MERQURY/plot/plot_spectra_cn.R -f $hist -o $name.spectra-asm -z $hist_asm_dist_only
+Rscript $MERQURY/plot/plot_spectra_cn.R -f $hist -o $name.spectra-asm -z $hist_asm_dist_only
 echo
 
 echo "Clean up"
diff --git a/programs/merqury_June2020/example/README.txt b/programs/merqury-1.1/example/README.txt
similarity index 100%
rename from programs/merqury_June2020/example/README.txt
rename to programs/merqury-1.1/example/README.txt
diff --git a/programs/merqury_June2020/example/inherited_hapmers.fl.png b/programs/merqury-1.1/example/inherited_hapmers.fl.png
similarity index 100%
rename from programs/merqury_June2020/example/inherited_hapmers.fl.png
rename to programs/merqury-1.1/example/inherited_hapmers.fl.png
diff --git a/programs/merqury_June2020/example/inherited_hapmers.ln.png b/programs/merqury-1.1/example/inherited_hapmers.ln.png
similarity index 100%
rename from programs/merqury_June2020/example/inherited_hapmers.ln.png
rename to programs/merqury-1.1/example/inherited_hapmers.ln.png
diff --git a/programs/merqury_June2020/example/inherited_hapmers.st.png b/programs/merqury-1.1/example/inherited_hapmers.st.png
similarity index 100%
rename from programs/merqury_June2020/example/inherited_hapmers.st.png
rename to programs/merqury-1.1/example/inherited_hapmers.st.png
diff --git a/programs/merqury_June2020/example/triocanu_clr.100_20000.col.block.N.png b/programs/merqury-1.1/example/triocanu_clr.100_20000.col.block.N.png
similarity index 100%
rename from programs/merqury_June2020/example/triocanu_clr.100_20000.col.block.N.png
rename to programs/merqury-1.1/example/triocanu_clr.100_20000.col.block.N.png
diff --git a/programs/merqury_June2020/example/triocanu_clr.100_20000.col.continuity.N.png b/programs/merqury-1.1/example/triocanu_clr.100_20000.col.continuity.N.png
similarity index 100%
rename from programs/merqury_June2020/example/triocanu_clr.100_20000.col.continuity.N.png
rename to programs/merqury-1.1/example/triocanu_clr.100_20000.col.continuity.N.png
diff --git a/programs/merqury_June2020/example/triocanu_clr.100_20000.cvi.block.N.png b/programs/merqury-1.1/example/triocanu_clr.100_20000.cvi.block.N.png
similarity index 100%
rename from programs/merqury_June2020/example/triocanu_clr.100_20000.cvi.block.N.png
rename to programs/merqury-1.1/example/triocanu_clr.100_20000.cvi.block.N.png
diff --git a/programs/merqury_June2020/example/triocanu_clr.100_20000.cvi.continuity.N.png b/programs/merqury-1.1/example/triocanu_clr.100_20000.cvi.continuity.N.png
similarity index 100%
rename from programs/merqury_June2020/example/triocanu_clr.100_20000.cvi.continuity.N.png
rename to programs/merqury-1.1/example/triocanu_clr.100_20000.cvi.continuity.N.png
diff --git a/programs/merqury_June2020/example/triocanu_clr.10_20000.col.block.N.png b/programs/merqury-1.1/example/triocanu_clr.10_20000.col.block.N.png
similarity index 100%
rename from programs/merqury_June2020/example/triocanu_clr.10_20000.col.block.N.png
rename to programs/merqury-1.1/example/triocanu_clr.10_20000.col.block.N.png
diff --git a/programs/merqury_June2020/example/triocanu_clr.10_20000.col.continuity.N.png b/programs/merqury-1.1/example/triocanu_clr.10_20000.col.continuity.N.png
similarity index 100%
rename from programs/merqury_June2020/example/triocanu_clr.10_20000.col.continuity.N.png
rename to programs/merqury-1.1/example/triocanu_clr.10_20000.col.continuity.N.png
diff --git a/programs/merqury_June2020/example/triocanu_clr.10_20000.cvi.block.N.png b/programs/merqury-1.1/example/triocanu_clr.10_20000.cvi.block.N.png
similarity index 100%
rename from programs/merqury_June2020/example/triocanu_clr.10_20000.cvi.block.N.png
rename to programs/merqury-1.1/example/triocanu_clr.10_20000.cvi.block.N.png
diff --git a/programs/merqury_June2020/example/triocanu_clr.10_20000.cvi.continuity.N.png b/programs/merqury-1.1/example/triocanu_clr.10_20000.cvi.continuity.N.png
similarity index 100%
rename from programs/merqury_June2020/example/triocanu_clr.10_20000.cvi.continuity.N.png
rename to programs/merqury-1.1/example/triocanu_clr.10_20000.cvi.continuity.N.png
diff --git a/programs/merqury_June2020/example/triocanu_clr.col.10_20000.phased_block.blob.png b/programs/merqury-1.1/example/triocanu_clr.col.10_20000.phased_block.blob.png
similarity index 100%
rename from programs/merqury_June2020/example/triocanu_clr.col.10_20000.phased_block.blob.png
rename to programs/merqury-1.1/example/triocanu_clr.col.10_20000.phased_block.blob.png
diff --git a/programs/merqury_June2020/example/triocanu_clr.col.block.N.png b/programs/merqury-1.1/example/triocanu_clr.col.block.N.png
similarity index 100%
rename from programs/merqury_June2020/example/triocanu_clr.col.block.N.png
rename to programs/merqury-1.1/example/triocanu_clr.col.block.N.png
diff --git a/programs/merqury_June2020/example/triocanu_clr.col.col0.hapmer.spectra-cn.fl.png b/programs/merqury-1.1/example/triocanu_clr.col.col0.hapmer.spectra-cn.fl.png
similarity index 100%
rename from programs/merqury_June2020/example/triocanu_clr.col.col0.hapmer.spectra-cn.fl.png
rename to programs/merqury-1.1/example/triocanu_clr.col.col0.hapmer.spectra-cn.fl.png
diff --git a/programs/merqury_June2020/example/triocanu_clr.col.col0.hapmer.spectra-cn.ln.png b/programs/merqury-1.1/example/triocanu_clr.col.col0.hapmer.spectra-cn.ln.png
similarity index 100%
rename from programs/merqury_June2020/example/triocanu_clr.col.col0.hapmer.spectra-cn.ln.png
rename to programs/merqury-1.1/example/triocanu_clr.col.col0.hapmer.spectra-cn.ln.png
diff --git a/programs/merqury_June2020/example/triocanu_clr.col.col0.hapmer.spectra-cn.st.png b/programs/merqury-1.1/example/triocanu_clr.col.col0.hapmer.spectra-cn.st.png
similarity index 100%
rename from programs/merqury_June2020/example/triocanu_clr.col.col0.hapmer.spectra-cn.st.png
rename to programs/merqury-1.1/example/triocanu_clr.col.col0.hapmer.spectra-cn.st.png
diff --git a/programs/merqury_June2020/example/triocanu_clr.col.continuity.N.png b/programs/merqury-1.1/example/triocanu_clr.col.continuity.N.png
similarity index 100%
rename from programs/merqury_June2020/example/triocanu_clr.col.continuity.N.png
rename to programs/merqury-1.1/example/triocanu_clr.col.continuity.N.png
diff --git a/programs/merqury_June2020/example/triocanu_clr.col.cvi0.hapmer.spectra-cn.fl.png b/programs/merqury-1.1/example/triocanu_clr.col.cvi0.hapmer.spectra-cn.fl.png
similarity index 100%
rename from programs/merqury_June2020/example/triocanu_clr.col.cvi0.hapmer.spectra-cn.fl.png
rename to programs/merqury-1.1/example/triocanu_clr.col.cvi0.hapmer.spectra-cn.fl.png
diff --git a/programs/merqury_June2020/example/triocanu_clr.col.cvi0.hapmer.spectra-cn.ln.png b/programs/merqury-1.1/example/triocanu_clr.col.cvi0.hapmer.spectra-cn.ln.png
similarity index 100%
rename from programs/merqury_June2020/example/triocanu_clr.col.cvi0.hapmer.spectra-cn.ln.png
rename to programs/merqury-1.1/example/triocanu_clr.col.cvi0.hapmer.spectra-cn.ln.png
diff --git a/programs/merqury_June2020/example/triocanu_clr.col.cvi0.hapmer.spectra-cn.st.png b/programs/merqury-1.1/example/triocanu_clr.col.cvi0.hapmer.spectra-cn.st.png
similarity index 100%
rename from programs/merqury_June2020/example/triocanu_clr.col.cvi0.hapmer.spectra-cn.st.png
rename to programs/merqury-1.1/example/triocanu_clr.col.cvi0.hapmer.spectra-cn.st.png
diff --git a/programs/merqury_June2020/example/triocanu_clr.col.spectra-cn.fl.png b/programs/merqury-1.1/example/triocanu_clr.col.spectra-cn.fl.png
similarity index 100%
rename from programs/merqury_June2020/example/triocanu_clr.col.spectra-cn.fl.png
rename to programs/merqury-1.1/example/triocanu_clr.col.spectra-cn.fl.png
diff --git a/programs/merqury_June2020/example/triocanu_clr.col.spectra-cn.ln.png b/programs/merqury-1.1/example/triocanu_clr.col.spectra-cn.ln.png
similarity index 100%
rename from programs/merqury_June2020/example/triocanu_clr.col.spectra-cn.ln.png
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diff --git a/programs/merqury_June2020/example/triocanu_clr.col.spectra-cn.st.png b/programs/merqury-1.1/example/triocanu_clr.col.spectra-cn.st.png
similarity index 100%
rename from programs/merqury_June2020/example/triocanu_clr.col.spectra-cn.st.png
rename to programs/merqury-1.1/example/triocanu_clr.col.spectra-cn.st.png
diff --git a/programs/merqury_June2020/example/triocanu_clr.cvi.10_20000.phased_block.blob.png b/programs/merqury-1.1/example/triocanu_clr.cvi.10_20000.phased_block.blob.png
similarity index 100%
rename from programs/merqury_June2020/example/triocanu_clr.cvi.10_20000.phased_block.blob.png
rename to programs/merqury-1.1/example/triocanu_clr.cvi.10_20000.phased_block.blob.png
diff --git a/programs/merqury_June2020/example/triocanu_clr.cvi.block.N.png b/programs/merqury-1.1/example/triocanu_clr.cvi.block.N.png
similarity index 100%
rename from programs/merqury_June2020/example/triocanu_clr.cvi.block.N.png
rename to programs/merqury-1.1/example/triocanu_clr.cvi.block.N.png
diff --git a/programs/merqury_June2020/example/triocanu_clr.cvi.col0.hapmer.spectra-cn.fl.png b/programs/merqury-1.1/example/triocanu_clr.cvi.col0.hapmer.spectra-cn.fl.png
similarity index 100%
rename from programs/merqury_June2020/example/triocanu_clr.cvi.col0.hapmer.spectra-cn.fl.png
rename to programs/merqury-1.1/example/triocanu_clr.cvi.col0.hapmer.spectra-cn.fl.png
diff --git a/programs/merqury_June2020/example/triocanu_clr.cvi.col0.hapmer.spectra-cn.ln.png b/programs/merqury-1.1/example/triocanu_clr.cvi.col0.hapmer.spectra-cn.ln.png
similarity index 100%
rename from programs/merqury_June2020/example/triocanu_clr.cvi.col0.hapmer.spectra-cn.ln.png
rename to programs/merqury-1.1/example/triocanu_clr.cvi.col0.hapmer.spectra-cn.ln.png
diff --git a/programs/merqury_June2020/example/triocanu_clr.cvi.col0.hapmer.spectra-cn.st.png b/programs/merqury-1.1/example/triocanu_clr.cvi.col0.hapmer.spectra-cn.st.png
similarity index 100%
rename from programs/merqury_June2020/example/triocanu_clr.cvi.col0.hapmer.spectra-cn.st.png
rename to programs/merqury-1.1/example/triocanu_clr.cvi.col0.hapmer.spectra-cn.st.png
diff --git a/programs/merqury_June2020/example/triocanu_clr.cvi.continuity.N.png b/programs/merqury-1.1/example/triocanu_clr.cvi.continuity.N.png
similarity index 100%
rename from programs/merqury_June2020/example/triocanu_clr.cvi.continuity.N.png
rename to programs/merqury-1.1/example/triocanu_clr.cvi.continuity.N.png
diff --git a/programs/merqury_June2020/example/triocanu_clr.cvi.cvi0.hapmer.spectra-cn.fl.png b/programs/merqury-1.1/example/triocanu_clr.cvi.cvi0.hapmer.spectra-cn.fl.png
similarity index 100%
rename from programs/merqury_June2020/example/triocanu_clr.cvi.cvi0.hapmer.spectra-cn.fl.png
rename to programs/merqury-1.1/example/triocanu_clr.cvi.cvi0.hapmer.spectra-cn.fl.png
diff --git a/programs/merqury_June2020/example/triocanu_clr.cvi.cvi0.hapmer.spectra-cn.ln.png b/programs/merqury-1.1/example/triocanu_clr.cvi.cvi0.hapmer.spectra-cn.ln.png
similarity index 100%
rename from programs/merqury_June2020/example/triocanu_clr.cvi.cvi0.hapmer.spectra-cn.ln.png
rename to programs/merqury-1.1/example/triocanu_clr.cvi.cvi0.hapmer.spectra-cn.ln.png
diff --git a/programs/merqury_June2020/example/triocanu_clr.cvi.cvi0.hapmer.spectra-cn.st.png b/programs/merqury-1.1/example/triocanu_clr.cvi.cvi0.hapmer.spectra-cn.st.png
similarity index 100%
rename from programs/merqury_June2020/example/triocanu_clr.cvi.cvi0.hapmer.spectra-cn.st.png
rename to programs/merqury-1.1/example/triocanu_clr.cvi.cvi0.hapmer.spectra-cn.st.png
diff --git a/programs/merqury_June2020/example/triocanu_clr.cvi.spectra-cn.fl.png b/programs/merqury-1.1/example/triocanu_clr.cvi.spectra-cn.fl.png
similarity index 100%
rename from programs/merqury_June2020/example/triocanu_clr.cvi.spectra-cn.fl.png
rename to programs/merqury-1.1/example/triocanu_clr.cvi.spectra-cn.fl.png
diff --git a/programs/merqury_June2020/example/triocanu_clr.cvi.spectra-cn.ln.png b/programs/merqury-1.1/example/triocanu_clr.cvi.spectra-cn.ln.png
similarity index 100%
rename from programs/merqury_June2020/example/triocanu_clr.cvi.spectra-cn.ln.png
rename to programs/merqury-1.1/example/triocanu_clr.cvi.spectra-cn.ln.png
diff --git a/programs/merqury_June2020/example/triocanu_clr.cvi.spectra-cn.st.png b/programs/merqury-1.1/example/triocanu_clr.cvi.spectra-cn.st.png
similarity index 100%
rename from programs/merqury_June2020/example/triocanu_clr.cvi.spectra-cn.st.png
rename to programs/merqury-1.1/example/triocanu_clr.cvi.spectra-cn.st.png
diff --git a/programs/merqury_June2020/example/triocanu_clr.hapmers.blob.png b/programs/merqury-1.1/example/triocanu_clr.hapmers.blob.png
similarity index 100%
rename from programs/merqury_June2020/example/triocanu_clr.hapmers.blob.png
rename to programs/merqury-1.1/example/triocanu_clr.hapmers.blob.png
diff --git a/programs/merqury_June2020/example/triocanu_clr.spectra-asm.fl.png b/programs/merqury-1.1/example/triocanu_clr.spectra-asm.fl.png
similarity index 100%
rename from programs/merqury_June2020/example/triocanu_clr.spectra-asm.fl.png
rename to programs/merqury-1.1/example/triocanu_clr.spectra-asm.fl.png
diff --git a/programs/merqury_June2020/example/triocanu_clr.spectra-asm.ln.png b/programs/merqury-1.1/example/triocanu_clr.spectra-asm.ln.png
similarity index 100%
rename from programs/merqury_June2020/example/triocanu_clr.spectra-asm.ln.png
rename to programs/merqury-1.1/example/triocanu_clr.spectra-asm.ln.png
diff --git a/programs/merqury_June2020/example/triocanu_clr.spectra-asm.st.png b/programs/merqury-1.1/example/triocanu_clr.spectra-asm.st.png
similarity index 100%
rename from programs/merqury_June2020/example/triocanu_clr.spectra-asm.st.png
rename to programs/merqury-1.1/example/triocanu_clr.spectra-asm.st.png
diff --git a/programs/merqury_June2020/example/triocanu_clr.spectra-cn.fl.png b/programs/merqury-1.1/example/triocanu_clr.spectra-cn.fl.png
similarity index 100%
rename from programs/merqury_June2020/example/triocanu_clr.spectra-cn.fl.png
rename to programs/merqury-1.1/example/triocanu_clr.spectra-cn.fl.png
diff --git a/programs/merqury_June2020/example/triocanu_clr.spectra-cn.ln.png b/programs/merqury-1.1/example/triocanu_clr.spectra-cn.ln.png
similarity index 100%
rename from programs/merqury_June2020/example/triocanu_clr.spectra-cn.ln.png
rename to programs/merqury-1.1/example/triocanu_clr.spectra-cn.ln.png
diff --git a/programs/merqury_June2020/example/triocanu_clr.spectra-cn.st.png b/programs/merqury-1.1/example/triocanu_clr.spectra-cn.st.png
similarity index 100%
rename from programs/merqury_June2020/example/triocanu_clr.spectra-cn.st.png
rename to programs/merqury-1.1/example/triocanu_clr.spectra-cn.st.png
diff --git a/programs/merqury_June2020/merqury-mash.sh b/programs/merqury-1.1/merqury-mash.sh
similarity index 81%
rename from programs/merqury_June2020/merqury-mash.sh
rename to programs/merqury-1.1/merqury-mash.sh
index d7b4372e391c592adc86e1d168c47192ae870a0a..8788b464dc53f227719406d37a655e0cbf593757 100755
--- a/programs/merqury_June2020/merqury-mash.sh
+++ b/programs/merqury-1.1/merqury-mash.sh
@@ -15,7 +15,15 @@ input_fofn=$3
 cpus=$4
 
 name=`echo $asm | sed 's/.fasta$//g' | sed 's/.fa$//g' | sed 's/.fasta.gz//g' | sed 's/.fa.gz//g'`
-module load mash
+
+source $MERQURY/util/util.sh
+
+has_module=$(check_module)
+if [[ $has_module -gt 0 ]]; then
+        echo "No modules available.."
+else
+        module load mash
+fi
 
 mash sketch -s 1000000 -k $k $asm
 mash screen -p $cpus $asm.msh `cat $input_fofn | tr '\n' ' '` > $name.msh.idy
diff --git a/programs/merqury_June2020/merqury.sh b/programs/merqury-1.1/merqury.sh
similarity index 100%
rename from programs/merqury_June2020/merqury.sh
rename to programs/merqury-1.1/merqury.sh
diff --git a/programs/merqury_June2020/plot/plot_blob.R b/programs/merqury-1.1/plot/plot_blob.R
similarity index 100%
rename from programs/merqury_June2020/plot/plot_blob.R
rename to programs/merqury-1.1/plot/plot_blob.R
diff --git a/programs/merqury_June2020/plot/plot_block_N.R b/programs/merqury-1.1/plot/plot_block_N.R
similarity index 100%
rename from programs/merqury_June2020/plot/plot_block_N.R
rename to programs/merqury-1.1/plot/plot_block_N.R
diff --git a/programs/merqury_June2020/plot/plot_spectra_asm.R b/programs/merqury-1.1/plot/plot_spectra_asm.R
similarity index 100%
rename from programs/merqury_June2020/plot/plot_spectra_asm.R
rename to programs/merqury-1.1/plot/plot_spectra_asm.R
diff --git a/programs/merqury_June2020/plot/plot_spectra_cn.R b/programs/merqury-1.1/plot/plot_spectra_cn.R
similarity index 100%
rename from programs/merqury_June2020/plot/plot_spectra_cn.R
rename to programs/merqury-1.1/plot/plot_spectra_cn.R
diff --git a/programs/merqury_June2020/trio/bedMerToPhaseBlock.jar b/programs/merqury-1.1/trio/bedMerToPhaseBlock.jar
similarity index 100%
rename from programs/merqury_June2020/trio/bedMerToPhaseBlock.jar
rename to programs/merqury-1.1/trio/bedMerToPhaseBlock.jar
diff --git a/programs/merqury_June2020/trio/block_n_stats.sh b/programs/merqury-1.1/trio/block_n_stats.sh
similarity index 96%
rename from programs/merqury_June2020/trio/block_n_stats.sh
rename to programs/merqury-1.1/trio/block_n_stats.sh
index ae7eadbc484dee0123ee03e0433af97eb1dcc5a8..af85ef5a1a7f0b6912af581f9a23f9db6f582370 100755
--- a/programs/merqury_June2020/trio/block_n_stats.sh
+++ b/programs/merqury-1.1/trio/block_n_stats.sh
@@ -65,7 +65,7 @@ do
     if [[ $num_gaps -gt 0 ]]; then
         echo "# Found $num_gaps. Generating stats for both scaffolds and contigs."
         awk -v asm=$asm '{print "scaffold\t"asm"\t"$2}' $asm.fasta.fai | sort -nr -k3 - > $out.$asm.scaff.sizes
-        awk '{print $1"\t0\t"$2}' $asm.fasta.fai | bedtools subtract -a - -b $asm.gaps.bed | awk '{print "contig\t"asm"\t"($NF-$(NF-1))}' | sort -nr -k3 - > $out.$asm.contig.sizes
+        awk '{print $1"\t0\t"$2}' $asm.fasta.fai | bedtools subtract -a - -b $asm.gaps.bed | awk -v asm=$asm '{print "contig\t"asm"\t"($NF-$(NF-1))}' | sort -nr -k3 - > $out.$asm.contig.sizes
     else
         echo "# No gaps found. This is a contig set."
         awk -v asm=$asm '{print "contig\t"asm"\t"$2}' $asm.fasta.fai | sort -nr -k3 - > $out.$asm.contig.sizes
diff --git a/programs/merqury_June2020/trio/exclude_reads.sh b/programs/merqury-1.1/trio/exclude_reads.sh
similarity index 100%
rename from programs/merqury_June2020/trio/exclude_reads.sh
rename to programs/merqury-1.1/trio/exclude_reads.sh
diff --git a/programs/merqury_June2020/trio/fastaGetGaps.jar b/programs/merqury-1.1/trio/fastaGetGaps.jar
similarity index 100%
rename from programs/merqury_June2020/trio/fastaGetGaps.jar
rename to programs/merqury-1.1/trio/fastaGetGaps.jar
diff --git a/programs/merqury_June2020/trio/hap_blob.sh b/programs/merqury-1.1/trio/hap_blob.sh
similarity index 100%
rename from programs/merqury_June2020/trio/hap_blob.sh
rename to programs/merqury-1.1/trio/hap_blob.sh
diff --git a/programs/merqury_June2020/trio/hapmers.sh b/programs/merqury-1.1/trio/hapmers.sh
similarity index 97%
rename from programs/merqury_June2020/trio/hapmers.sh
rename to programs/merqury-1.1/trio/hapmers.sh
index 6e4551cce9a85c2f22753ef59c9fc67c1bb55b95..aeaa48f24817fbd575c6be5480d59331d281e770 100755
--- a/programs/merqury_June2020/trio/hapmers.sh
+++ b/programs/merqury-1.1/trio/hapmers.sh
@@ -22,9 +22,11 @@ if [[ "$#" -lt 2 ]]; then
 	exit -1
 fi
 
-hap1_meryl=$1
-hap2_meryl=$2
-child_meryl=$3
+source $MERQURY/util/util.sh
+
+hap1_meryl=`link $1`
+hap2_meryl=`link $2`
+child_meryl=`link $3`
 
 hap1=${hap1_meryl%.meryl*}
 hap2=${hap2_meryl%.meryl*}
diff --git a/programs/merqury-1.1/trio/hapmers_to_bigwig.sh b/programs/merqury-1.1/trio/hapmers_to_bigwig.sh
new file mode 100755
index 0000000000000000000000000000000000000000..4b208ac816e5064a2c6d5e68acf8d4be48c3ca0f
--- /dev/null
+++ b/programs/merqury-1.1/trio/hapmers_to_bigwig.sh
@@ -0,0 +1,38 @@
+#!/bin/bash
+
+if [[ -z $1 ]]; then
+    echo "Usage: ./hapmers_to_bigWig.sh <in.hap.bed> <asm.fai> [convert_pipes]"
+    echo -e "\t<in.hap.bed>: ex. out.asm.mat.inherited.bed"
+    echo -e "\t<asm.fai>: generate with samtools faidx"
+    echo -e "\t[convert_pipes]: convert '|' to '_' in asm seq names by default. Set to F if not wanted."
+    exit 0
+fi
+
+bed=$1
+fai=$2
+convert=$3
+
+module load bedtools
+module load ucsc/396
+
+bg=${bed/.bed/.bg}
+
+if [[ "$convert" = "F" ]]; then
+    echo "# keep pipes"
+    sizes=${fai/.fai/.sizes}
+    cat $fai | cut -f1-2 > $sizes
+    cat $bed | bedtools genomecov -bg -g $sizes -i - > $bg
+else
+    sizes=${fai/.fai/.sizes}
+    cat $fai | cut -f1-2 | sed 's/|/_/g' > $sizes
+    cat $bed | sed 's/|/_/g' | bedtools genomecov -bg -g $sizes -i - > $bg
+fi
+
+sort=${bg/.bg/.srt.bg}
+bedSort $bg $sort
+
+bw=${bed/.bed/.bigwig}
+bedGraphToBigWig $sort $sizes $bw
+
+rm $bg $sort
+
diff --git a/programs/merqury_June2020/trio/phase_block.sh b/programs/merqury-1.1/trio/phase_block.sh
similarity index 100%
rename from programs/merqury_June2020/trio/phase_block.sh
rename to programs/merqury-1.1/trio/phase_block.sh
diff --git a/programs/merqury_June2020/trio/phase_block/IO/Rwrapper.java b/programs/merqury-1.1/trio/phase_block/IO/Rwrapper.java
similarity index 100%
rename from programs/merqury_June2020/trio/phase_block/IO/Rwrapper.java
rename to programs/merqury-1.1/trio/phase_block/IO/Rwrapper.java
diff --git a/programs/merqury_June2020/trio/phase_block/IO/basic/BufferedFileReader.java b/programs/merqury-1.1/trio/phase_block/IO/basic/BufferedFileReader.java
similarity index 100%
rename from programs/merqury_June2020/trio/phase_block/IO/basic/BufferedFileReader.java
rename to programs/merqury-1.1/trio/phase_block/IO/basic/BufferedFileReader.java
diff --git a/programs/merqury_June2020/trio/phase_block/IO/basic/FileMaker.java b/programs/merqury-1.1/trio/phase_block/IO/basic/FileMaker.java
similarity index 100%
rename from programs/merqury_June2020/trio/phase_block/IO/basic/FileMaker.java
rename to programs/merqury-1.1/trio/phase_block/IO/basic/FileMaker.java
diff --git a/programs/merqury_June2020/trio/phase_block/IO/basic/FileReader.java b/programs/merqury-1.1/trio/phase_block/IO/basic/FileReader.java
similarity index 100%
rename from programs/merqury_June2020/trio/phase_block/IO/basic/FileReader.java
rename to programs/merqury-1.1/trio/phase_block/IO/basic/FileReader.java
diff --git a/programs/merqury_June2020/trio/phase_block/IO/basic/Format.java b/programs/merqury-1.1/trio/phase_block/IO/basic/Format.java
similarity index 100%
rename from programs/merqury_June2020/trio/phase_block/IO/basic/Format.java
rename to programs/merqury-1.1/trio/phase_block/IO/basic/Format.java
diff --git a/programs/merqury_June2020/trio/phase_block/IO/basic/IOUtil.java b/programs/merqury-1.1/trio/phase_block/IO/basic/IOUtil.java
similarity index 100%
rename from programs/merqury_June2020/trio/phase_block/IO/basic/IOUtil.java
rename to programs/merqury-1.1/trio/phase_block/IO/basic/IOUtil.java
diff --git a/programs/merqury_June2020/trio/phase_block/IO/basic/RegExp.java b/programs/merqury-1.1/trio/phase_block/IO/basic/RegExp.java
similarity index 100%
rename from programs/merqury_June2020/trio/phase_block/IO/basic/RegExp.java
rename to programs/merqury-1.1/trio/phase_block/IO/basic/RegExp.java
diff --git a/programs/merqury_June2020/trio/phase_block/IO/basic/Wrapper.java b/programs/merqury-1.1/trio/phase_block/IO/basic/Wrapper.java
similarity index 100%
rename from programs/merqury_June2020/trio/phase_block/IO/basic/Wrapper.java
rename to programs/merqury-1.1/trio/phase_block/IO/basic/Wrapper.java
diff --git a/programs/merqury_June2020/trio/phase_block/MerToPhaseBlock.java b/programs/merqury-1.1/trio/phase_block/MerToPhaseBlock.java
similarity index 100%
rename from programs/merqury_June2020/trio/phase_block/MerToPhaseBlock.java
rename to programs/merqury-1.1/trio/phase_block/MerToPhaseBlock.java
diff --git a/programs/merqury_June2020/trio/phase_block/README.md b/programs/merqury-1.1/trio/phase_block/README.md
similarity index 100%
rename from programs/merqury_June2020/trio/phase_block/README.md
rename to programs/merqury-1.1/trio/phase_block/README.md
diff --git a/programs/merqury_June2020/trio/phase_block/bed/util/Bed.java b/programs/merqury-1.1/trio/phase_block/bed/util/Bed.java
similarity index 100%
rename from programs/merqury_June2020/trio/phase_block/bed/util/Bed.java
rename to programs/merqury-1.1/trio/phase_block/bed/util/Bed.java
diff --git a/programs/merqury_June2020/trio/phase_block/bed/util/Region.java b/programs/merqury-1.1/trio/phase_block/bed/util/Region.java
similarity index 100%
rename from programs/merqury_June2020/trio/phase_block/bed/util/Region.java
rename to programs/merqury-1.1/trio/phase_block/bed/util/Region.java
diff --git a/programs/merqury_June2020/trio/phase_block/build_jar.sh b/programs/merqury-1.1/trio/phase_block/build_jar.sh
similarity index 100%
rename from programs/merqury_June2020/trio/phase_block/build_jar.sh
rename to programs/merqury-1.1/trio/phase_block/build_jar.sh
diff --git a/programs/merqury_June2020/trio/phase_block/genome/Chromosome.java b/programs/merqury-1.1/trio/phase_block/genome/Chromosome.java
similarity index 100%
rename from programs/merqury_June2020/trio/phase_block/genome/Chromosome.java
rename to programs/merqury-1.1/trio/phase_block/genome/Chromosome.java
diff --git a/programs/merqury_June2020/trio/phase_block/genome/ChromosomeComparator.java b/programs/merqury-1.1/trio/phase_block/genome/ChromosomeComparator.java
similarity index 100%
rename from programs/merqury_June2020/trio/phase_block/genome/ChromosomeComparator.java
rename to programs/merqury-1.1/trio/phase_block/genome/ChromosomeComparator.java
diff --git a/programs/merqury_June2020/trio/phase_block/genome/util/Util.java b/programs/merqury-1.1/trio/phase_block/genome/util/Util.java
similarity index 100%
rename from programs/merqury_June2020/trio/phase_block/genome/util/Util.java
rename to programs/merqury-1.1/trio/phase_block/genome/util/Util.java
diff --git a/programs/merqury_June2020/trio/spectra-hap.sh b/programs/merqury-1.1/trio/spectra-hap.sh
similarity index 100%
rename from programs/merqury_June2020/trio/spectra-hap.sh
rename to programs/merqury-1.1/trio/spectra-hap.sh
diff --git a/programs/merqury_June2020/trio/switch_error.sh b/programs/merqury-1.1/trio/switch_error.sh
similarity index 100%
rename from programs/merqury_June2020/trio/switch_error.sh
rename to programs/merqury-1.1/trio/switch_error.sh
diff --git a/programs/merqury-1.1/util/bed_to_bigwig.sh b/programs/merqury-1.1/util/bed_to_bigwig.sh
new file mode 100755
index 0000000000000000000000000000000000000000..fcc554b508f6580b2a039c7a91b1278a3fa62b63
--- /dev/null
+++ b/programs/merqury-1.1/util/bed_to_bigwig.sh
@@ -0,0 +1,39 @@
+#!/bin/bash
+
+if [[ -z $1 ]]; then
+    echo "Usage: ./bed_to_bigWig.sh <bed> <asm.fai> <convert_pipes>"
+    echo -e "\t<bed>: ex. out.asm.mat.inherited.bed"
+    echo -e "\t<asm.fai>: generate with samtools faidx"
+    echo -e "\t<convert_pipes>: convert | to _ by default. Set to F if not wanted."
+    exit 0
+fi
+
+bed=$1
+fai=$2
+convert=$3
+
+module load bedtools
+module load ucsc/396
+
+bg=${bed/.bed/.bg}
+
+if [[ "$convert" = "F" ]]; then
+    echo "# keep pipes"
+    sizes=${fai/.fai/.sizes}
+    cat $fai | cut -f1-2 > $sizes
+    cat $bed | bedtools genomecov -bg -g $sizes -i - > $bg
+else
+    sizes=${fai/.fai/.sizes}
+    cat $fai | cut -f1-2 | sed 's/|/_/g' > $sizes
+    cat $bed | sed 's/|/_/g' | bedtools genomecov -bg -g $sizes -i - > $bg
+fi
+
+sort=${bg/.bg/.srt.bg}
+bedSort $bg $sort
+
+bw=${bed/.bed/.bigwig}
+bedGraphToBigWig $sort $sizes $bw
+
+rm $bg $sort
+
+
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rename from programs/merqury_June2020/util/util.sh
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