From 17e047dbbfac75cbeb0cec11248cc89cf294445b Mon Sep 17 00:00:00 2001
From: james94 <james94@mi.fu-berlin.de>
Date: Wed, 10 Mar 2021 20:26:26 +0100
Subject: [PATCH] to get running on HPC
---
envs/genomescope.yaml | 6 +
envs/merylMerq.yaml | 7 +-
programs/merqury-1.1/LICENSE | 19 ++
programs/merqury-1.1/README.md | 191 ++++++++++++++++++
.../_submit_build.sh | 6 +-
.../_submit_build_10x.sh | 2 +-
.../_submit_hapmers.sh | 0
.../_submit_merqury.sh | 0
.../_submit_split.sh | 0
.../best_k.sh | 0
.../build/concat_splits.sh | 0
.../build/count.sh | 0
.../build/count_10x.sh | 20 +-
.../build/diff.sh | 0
.../build/filt.sh | 0
.../build/intersect.sh | 0
.../build/split.sh | 5 +-
.../build/split_10x.sh | 10 +-
.../build/union_sum.sh | 10 -
programs/merqury-1.1/eval/asm_multiplicity.sh | 33 +++
.../eval/bedCalcN50.jar | Bin
.../merqury-1.1/eval/false_duplications.sh | 21 ++
.../eval/kmerHistToPloidyDepth.jar | Bin
programs/merqury-1.1/eval/per_seq_qv.sh | 43 ++++
.../eval/qv.sh | 8 +-
.../merqury-1.1/eval/read_multiplicity.sh | 31 +++
.../eval/spectra-cn.sh | 19 +-
.../example/README.txt | 0
.../example/inherited_hapmers.fl.png | Bin
.../example/inherited_hapmers.ln.png | Bin
.../example/inherited_hapmers.st.png | Bin
.../triocanu_clr.100_20000.col.block.N.png | Bin
...riocanu_clr.100_20000.col.continuity.N.png | Bin
.../triocanu_clr.100_20000.cvi.block.N.png | Bin
...riocanu_clr.100_20000.cvi.continuity.N.png | Bin
.../triocanu_clr.10_20000.col.block.N.png | Bin
...triocanu_clr.10_20000.col.continuity.N.png | Bin
.../triocanu_clr.10_20000.cvi.block.N.png | Bin
...triocanu_clr.10_20000.cvi.continuity.N.png | Bin
...anu_clr.col.10_20000.phased_block.blob.png | Bin
.../example/triocanu_clr.col.block.N.png | Bin
...canu_clr.col.col0.hapmer.spectra-cn.fl.png | Bin
...canu_clr.col.col0.hapmer.spectra-cn.ln.png | Bin
...canu_clr.col.col0.hapmer.spectra-cn.st.png | Bin
.../example/triocanu_clr.col.continuity.N.png | Bin
...canu_clr.col.cvi0.hapmer.spectra-cn.fl.png | Bin
...canu_clr.col.cvi0.hapmer.spectra-cn.ln.png | Bin
...canu_clr.col.cvi0.hapmer.spectra-cn.st.png | Bin
.../triocanu_clr.col.spectra-cn.fl.png | Bin
.../triocanu_clr.col.spectra-cn.ln.png | Bin
.../triocanu_clr.col.spectra-cn.st.png | Bin
...anu_clr.cvi.10_20000.phased_block.blob.png | Bin
.../example/triocanu_clr.cvi.block.N.png | Bin
...canu_clr.cvi.col0.hapmer.spectra-cn.fl.png | Bin
...canu_clr.cvi.col0.hapmer.spectra-cn.ln.png | Bin
...canu_clr.cvi.col0.hapmer.spectra-cn.st.png | Bin
.../example/triocanu_clr.cvi.continuity.N.png | Bin
...canu_clr.cvi.cvi0.hapmer.spectra-cn.fl.png | Bin
...canu_clr.cvi.cvi0.hapmer.spectra-cn.ln.png | Bin
...canu_clr.cvi.cvi0.hapmer.spectra-cn.st.png | Bin
.../triocanu_clr.cvi.spectra-cn.fl.png | Bin
.../triocanu_clr.cvi.spectra-cn.ln.png | Bin
.../triocanu_clr.cvi.spectra-cn.st.png | Bin
.../example/triocanu_clr.hapmers.blob.png | Bin
.../example/triocanu_clr.spectra-asm.fl.png | Bin
.../example/triocanu_clr.spectra-asm.ln.png | Bin
.../example/triocanu_clr.spectra-asm.st.png | Bin
.../example/triocanu_clr.spectra-cn.fl.png | Bin
.../example/triocanu_clr.spectra-cn.ln.png | Bin
.../example/triocanu_clr.spectra-cn.st.png | Bin
.../merqury-mash.sh | 10 +-
.../merqury.sh | 0
.../plot/plot_blob.R | 0
.../plot/plot_block_N.R | 0
.../plot/plot_spectra_asm.R | 0
.../plot/plot_spectra_cn.R | 0
.../trio/bedMerToPhaseBlock.jar | Bin
.../trio/block_n_stats.sh | 2 +-
.../trio/exclude_reads.sh | 0
.../trio/fastaGetGaps.jar | Bin
.../trio/hap_blob.sh | 0
.../trio/hapmers.sh | 8 +-
.../merqury-1.1/trio/hapmers_to_bigwig.sh | 38 ++++
.../trio/phase_block.sh | 0
.../trio/phase_block/IO/Rwrapper.java | 0
.../IO/basic/BufferedFileReader.java | 0
.../trio/phase_block/IO/basic/FileMaker.java | 0
.../trio/phase_block/IO/basic/FileReader.java | 0
.../trio/phase_block/IO/basic/Format.java | 0
.../trio/phase_block/IO/basic/IOUtil.java | 0
.../trio/phase_block/IO/basic/RegExp.java | 0
.../trio/phase_block/IO/basic/Wrapper.java | 0
.../trio/phase_block/MerToPhaseBlock.java | 0
.../trio/phase_block/README.md | 0
.../trio/phase_block/bed/util/Bed.java | 0
.../trio/phase_block/bed/util/Region.java | 0
.../trio/phase_block/build_jar.sh | 0
.../trio/phase_block/genome/Chromosome.java | 0
.../genome/ChromosomeComparator.java | 0
.../trio/phase_block/genome/util/Util.java | 0
.../trio/spectra-hap.sh | 0
.../trio/switch_error.sh | 0
programs/merqury-1.1/util/bed_to_bigwig.sh | 39 ++++
programs/merqury-1.1/util/merylDumpToWig.jar | Bin 0 -> 17892 bytes
.../util/util.sh | 0
programs/merqury_June2020/.DS_Store | Bin 6148 -> 0 bytes
programs/meryl-1.0/.DS_Store | Bin 6148 -> 0 bytes
107 files changed, 485 insertions(+), 43 deletions(-)
create mode 100644 envs/genomescope.yaml
create mode 100644 programs/merqury-1.1/LICENSE
create mode 100644 programs/merqury-1.1/README.md
rename programs/{merqury_June2020 => merqury-1.1}/_submit_build.sh (96%)
rename programs/{merqury_June2020 => merqury-1.1}/_submit_build_10x.sh (98%)
rename programs/{merqury_June2020 => merqury-1.1}/_submit_hapmers.sh (100%)
rename programs/{merqury_June2020 => merqury-1.1}/_submit_merqury.sh (100%)
rename programs/{merqury_June2020 => merqury-1.1}/_submit_split.sh (100%)
rename programs/{merqury_June2020 => merqury-1.1}/best_k.sh (100%)
rename programs/{merqury_June2020 => merqury-1.1}/build/concat_splits.sh (100%)
rename programs/{merqury_June2020 => merqury-1.1}/build/count.sh (100%)
rename programs/{merqury_June2020 => merqury-1.1}/build/count_10x.sh (74%)
rename programs/{merqury_June2020 => merqury-1.1}/build/diff.sh (100%)
rename programs/{merqury_June2020 => merqury-1.1}/build/filt.sh (100%)
rename programs/{merqury_June2020 => merqury-1.1}/build/intersect.sh (100%)
rename programs/{merqury_June2020 => merqury-1.1}/build/split.sh (91%)
rename programs/{merqury_June2020 => merqury-1.1}/build/split_10x.sh (87%)
rename programs/{merqury_June2020 => merqury-1.1}/build/union_sum.sh (90%)
create mode 100755 programs/merqury-1.1/eval/asm_multiplicity.sh
rename programs/{merqury_June2020 => merqury-1.1}/eval/bedCalcN50.jar (100%)
create mode 100755 programs/merqury-1.1/eval/false_duplications.sh
rename programs/{merqury_June2020 => merqury-1.1}/eval/kmerHistToPloidyDepth.jar (100%)
create mode 100755 programs/merqury-1.1/eval/per_seq_qv.sh
rename programs/{merqury_June2020 => merqury-1.1}/eval/qv.sh (87%)
create mode 100755 programs/merqury-1.1/eval/read_multiplicity.sh
rename programs/{merqury_June2020 => merqury-1.1}/eval/spectra-cn.sh (92%)
rename programs/{merqury_June2020 => merqury-1.1}/example/README.txt (100%)
rename programs/{merqury_June2020 => merqury-1.1}/example/inherited_hapmers.fl.png (100%)
rename programs/{merqury_June2020 => merqury-1.1}/example/inherited_hapmers.ln.png (100%)
rename programs/{merqury_June2020 => merqury-1.1}/example/inherited_hapmers.st.png (100%)
rename programs/{merqury_June2020 => merqury-1.1}/example/triocanu_clr.100_20000.col.block.N.png (100%)
rename programs/{merqury_June2020 => merqury-1.1}/example/triocanu_clr.100_20000.col.continuity.N.png (100%)
rename programs/{merqury_June2020 => merqury-1.1}/example/triocanu_clr.100_20000.cvi.block.N.png (100%)
rename programs/{merqury_June2020 => merqury-1.1}/example/triocanu_clr.100_20000.cvi.continuity.N.png (100%)
rename programs/{merqury_June2020 => merqury-1.1}/example/triocanu_clr.10_20000.col.block.N.png (100%)
rename programs/{merqury_June2020 => merqury-1.1}/example/triocanu_clr.10_20000.col.continuity.N.png (100%)
rename programs/{merqury_June2020 => merqury-1.1}/example/triocanu_clr.10_20000.cvi.block.N.png (100%)
rename programs/{merqury_June2020 => merqury-1.1}/example/triocanu_clr.10_20000.cvi.continuity.N.png (100%)
rename programs/{merqury_June2020 => merqury-1.1}/example/triocanu_clr.col.10_20000.phased_block.blob.png (100%)
rename programs/{merqury_June2020 => merqury-1.1}/example/triocanu_clr.col.block.N.png (100%)
rename programs/{merqury_June2020 => merqury-1.1}/example/triocanu_clr.col.col0.hapmer.spectra-cn.fl.png (100%)
rename programs/{merqury_June2020 => merqury-1.1}/example/triocanu_clr.col.col0.hapmer.spectra-cn.ln.png (100%)
rename programs/{merqury_June2020 => merqury-1.1}/example/triocanu_clr.col.col0.hapmer.spectra-cn.st.png (100%)
rename programs/{merqury_June2020 => merqury-1.1}/example/triocanu_clr.col.continuity.N.png (100%)
rename programs/{merqury_June2020 => merqury-1.1}/example/triocanu_clr.col.cvi0.hapmer.spectra-cn.fl.png (100%)
rename programs/{merqury_June2020 => merqury-1.1}/example/triocanu_clr.col.cvi0.hapmer.spectra-cn.ln.png (100%)
rename programs/{merqury_June2020 => merqury-1.1}/example/triocanu_clr.col.cvi0.hapmer.spectra-cn.st.png (100%)
rename programs/{merqury_June2020 => merqury-1.1}/example/triocanu_clr.col.spectra-cn.fl.png (100%)
rename programs/{merqury_June2020 => merqury-1.1}/example/triocanu_clr.col.spectra-cn.ln.png (100%)
rename programs/{merqury_June2020 => merqury-1.1}/example/triocanu_clr.col.spectra-cn.st.png (100%)
rename programs/{merqury_June2020 => merqury-1.1}/example/triocanu_clr.cvi.10_20000.phased_block.blob.png (100%)
rename programs/{merqury_June2020 => merqury-1.1}/example/triocanu_clr.cvi.block.N.png (100%)
rename programs/{merqury_June2020 => merqury-1.1}/example/triocanu_clr.cvi.col0.hapmer.spectra-cn.fl.png (100%)
rename programs/{merqury_June2020 => merqury-1.1}/example/triocanu_clr.cvi.col0.hapmer.spectra-cn.ln.png (100%)
rename programs/{merqury_June2020 => merqury-1.1}/example/triocanu_clr.cvi.col0.hapmer.spectra-cn.st.png (100%)
rename programs/{merqury_June2020 => merqury-1.1}/example/triocanu_clr.cvi.continuity.N.png (100%)
rename programs/{merqury_June2020 => merqury-1.1}/example/triocanu_clr.cvi.cvi0.hapmer.spectra-cn.fl.png (100%)
rename programs/{merqury_June2020 => merqury-1.1}/example/triocanu_clr.cvi.cvi0.hapmer.spectra-cn.ln.png (100%)
rename programs/{merqury_June2020 => merqury-1.1}/example/triocanu_clr.cvi.cvi0.hapmer.spectra-cn.st.png (100%)
rename programs/{merqury_June2020 => merqury-1.1}/example/triocanu_clr.cvi.spectra-cn.fl.png (100%)
rename programs/{merqury_June2020 => merqury-1.1}/example/triocanu_clr.cvi.spectra-cn.ln.png (100%)
rename programs/{merqury_June2020 => merqury-1.1}/example/triocanu_clr.cvi.spectra-cn.st.png (100%)
rename programs/{merqury_June2020 => merqury-1.1}/example/triocanu_clr.hapmers.blob.png (100%)
rename programs/{merqury_June2020 => merqury-1.1}/example/triocanu_clr.spectra-asm.fl.png (100%)
rename programs/{merqury_June2020 => merqury-1.1}/example/triocanu_clr.spectra-asm.ln.png (100%)
rename programs/{merqury_June2020 => merqury-1.1}/example/triocanu_clr.spectra-asm.st.png (100%)
rename programs/{merqury_June2020 => merqury-1.1}/example/triocanu_clr.spectra-cn.fl.png (100%)
rename programs/{merqury_June2020 => merqury-1.1}/example/triocanu_clr.spectra-cn.ln.png (100%)
rename programs/{merqury_June2020 => merqury-1.1}/example/triocanu_clr.spectra-cn.st.png (100%)
rename programs/{merqury_June2020 => merqury-1.1}/merqury-mash.sh (81%)
rename programs/{merqury_June2020 => merqury-1.1}/merqury.sh (100%)
rename programs/{merqury_June2020 => merqury-1.1}/plot/plot_blob.R (100%)
rename programs/{merqury_June2020 => merqury-1.1}/plot/plot_block_N.R (100%)
rename programs/{merqury_June2020 => merqury-1.1}/plot/plot_spectra_asm.R (100%)
rename programs/{merqury_June2020 => merqury-1.1}/plot/plot_spectra_cn.R (100%)
rename programs/{merqury_June2020 => merqury-1.1}/trio/bedMerToPhaseBlock.jar (100%)
rename programs/{merqury_June2020 => merqury-1.1}/trio/block_n_stats.sh (96%)
rename programs/{merqury_June2020 => merqury-1.1}/trio/exclude_reads.sh (100%)
rename programs/{merqury_June2020 => merqury-1.1}/trio/fastaGetGaps.jar (100%)
rename programs/{merqury_June2020 => merqury-1.1}/trio/hap_blob.sh (100%)
rename programs/{merqury_June2020 => merqury-1.1}/trio/hapmers.sh (97%)
create mode 100755 programs/merqury-1.1/trio/hapmers_to_bigwig.sh
rename programs/{merqury_June2020 => merqury-1.1}/trio/phase_block.sh (100%)
rename programs/{merqury_June2020 => merqury-1.1}/trio/phase_block/IO/Rwrapper.java (100%)
rename programs/{merqury_June2020 => merqury-1.1}/trio/phase_block/IO/basic/BufferedFileReader.java (100%)
rename programs/{merqury_June2020 => merqury-1.1}/trio/phase_block/IO/basic/FileMaker.java (100%)
rename programs/{merqury_June2020 => merqury-1.1}/trio/phase_block/IO/basic/FileReader.java (100%)
rename programs/{merqury_June2020 => merqury-1.1}/trio/phase_block/IO/basic/Format.java (100%)
rename programs/{merqury_June2020 => merqury-1.1}/trio/phase_block/IO/basic/IOUtil.java (100%)
rename programs/{merqury_June2020 => merqury-1.1}/trio/phase_block/IO/basic/RegExp.java (100%)
rename programs/{merqury_June2020 => merqury-1.1}/trio/phase_block/IO/basic/Wrapper.java (100%)
rename programs/{merqury_June2020 => merqury-1.1}/trio/phase_block/MerToPhaseBlock.java (100%)
rename programs/{merqury_June2020 => merqury-1.1}/trio/phase_block/README.md (100%)
rename programs/{merqury_June2020 => merqury-1.1}/trio/phase_block/bed/util/Bed.java (100%)
rename programs/{merqury_June2020 => merqury-1.1}/trio/phase_block/bed/util/Region.java (100%)
rename programs/{merqury_June2020 => merqury-1.1}/trio/phase_block/build_jar.sh (100%)
rename programs/{merqury_June2020 => merqury-1.1}/trio/phase_block/genome/Chromosome.java (100%)
rename programs/{merqury_June2020 => merqury-1.1}/trio/phase_block/genome/ChromosomeComparator.java (100%)
rename programs/{merqury_June2020 => merqury-1.1}/trio/phase_block/genome/util/Util.java (100%)
rename programs/{merqury_June2020 => merqury-1.1}/trio/spectra-hap.sh (100%)
rename programs/{merqury_June2020 => merqury-1.1}/trio/switch_error.sh (100%)
create mode 100755 programs/merqury-1.1/util/bed_to_bigwig.sh
create mode 100644 programs/merqury-1.1/util/merylDumpToWig.jar
rename programs/{merqury_June2020 => merqury-1.1}/util/util.sh (100%)
delete mode 100644 programs/merqury_June2020/.DS_Store
delete mode 100644 programs/meryl-1.0/.DS_Store
diff --git a/envs/genomescope.yaml b/envs/genomescope.yaml
new file mode 100644
index 0000000..e852490
--- /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 a7d2a4e..96c6aed 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 0000000..1696843
--- /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 0000000..4808a8c
--- /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 988e26d..e44a8b8 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$i,"
diff --git a/programs/merqury_June2020/_submit_build_10x.sh b/programs/merqury-1.1/_submit_build_10x.sh
similarity index 98%
rename from programs/merqury_June2020/_submit_build_10x.sh
rename to programs/merqury-1.1/_submit_build_10x.sh
index 6c424db..c1c9c42 100755
--- a/programs/merqury_June2020/_submit_build_10x.sh
+++ b/programs/merqury-1.1/_submit_build_10x.sh
@@ -1,6 +1,6 @@
#!/bin/bash
-build=/srv/public/users/tomas/programs/merqury/build
+build=$MERQURY/build
if [ -z $1 ]; then
echo "Usage: ./_submit_build.sh <k-size> <R1.fofn> <R2.fofn> <out_prefix> [mem=T]"
diff --git a/programs/merqury_June2020/_submit_hapmers.sh b/programs/merqury-1.1/_submit_hapmers.sh
similarity index 100%
rename from programs/merqury_June2020/_submit_hapmers.sh
rename to programs/merqury-1.1/_submit_hapmers.sh
diff --git a/programs/merqury_June2020/_submit_merqury.sh b/programs/merqury-1.1/_submit_merqury.sh
similarity index 100%
rename from programs/merqury_June2020/_submit_merqury.sh
rename to programs/merqury-1.1/_submit_merqury.sh
diff --git a/programs/merqury_June2020/_submit_split.sh b/programs/merqury-1.1/_submit_split.sh
similarity index 100%
rename from programs/merqury_June2020/_submit_split.sh
rename to programs/merqury-1.1/_submit_split.sh
diff --git a/programs/merqury_June2020/best_k.sh b/programs/merqury-1.1/best_k.sh
similarity index 100%
rename from programs/merqury_June2020/best_k.sh
rename to programs/merqury-1.1/best_k.sh
diff --git a/programs/merqury_June2020/build/concat_splits.sh b/programs/merqury-1.1/build/concat_splits.sh
similarity index 100%
rename from programs/merqury_June2020/build/concat_splits.sh
rename to programs/merqury-1.1/build/concat_splits.sh
diff --git a/programs/merqury_June2020/build/count.sh b/programs/merqury-1.1/build/count.sh
similarity index 100%
rename from programs/merqury_June2020/build/count.sh
rename to programs/merqury-1.1/build/count.sh
diff --git a/programs/merqury_June2020/build/count_10x.sh b/programs/merqury-1.1/build/count_10x.sh
similarity index 74%
rename from programs/merqury_June2020/build/count_10x.sh
rename to programs/merqury-1.1/build/count_10x.sh
index 8ec5736..1f5e226 100755
--- a/programs/merqury_June2020/build/count_10x.sh
+++ b/programs/merqury-1.1/build/count_10x.sh
@@ -28,9 +28,19 @@ else
line_num=$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 40e3980..9dca150 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 6654096..e125233 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 dc21905..a01c15e 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 $output_prefix.meryl \
diff --git a/programs/merqury-1.1/eval/asm_multiplicity.sh b/programs/merqury-1.1/eval/asm_multiplicity.sh
new file mode 100755
index 0000000..51ed3ec
--- /dev/null
+++ b/programs/merqury-1.1/eval/asm_multiplicity.sh
@@ -0,0 +1,33 @@
+#!/bin/sh
+
+if [[ "$#" -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 0000000..ed7bf0a
--- /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 0000000..9f0125d
--- /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))}' > $name.qv
+
diff --git a/programs/merqury_June2020/eval/qv.sh b/programs/merqury-1.1/eval/qv.sh
similarity index 87%
rename from programs/merqury_June2020/eval/qv.sh
rename to programs/merqury-1.1/eval/qv.sh
index bc37f00..c5ccdaf 100755
--- a/programs/merqury_June2020/eval/qv.sh
+++ b/programs/merqury-1.1/eval/qv.sh
@@ -50,6 +50,9 @@ do
QV=`echo "$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 $asm.meryl
echo "Done!"
+
diff --git a/programs/merqury-1.1/eval/read_multiplicity.sh b/programs/merqury-1.1/eval/read_multiplicity.sh
new file mode 100755
index 0000000..062add8
--- /dev/null
+++ b/programs/merqury-1.1/eval/read_multiplicity.sh
@@ -0,0 +1,31 @@
+#!/bin/sh
+
+if [[ "$#" -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 0338699..f528c47 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
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rename from programs/merqury_June2020/example/inherited_hapmers.ln.png
rename to programs/merqury-1.1/example/inherited_hapmers.ln.png
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rename from programs/merqury_June2020/example/inherited_hapmers.st.png
rename to programs/merqury-1.1/example/inherited_hapmers.st.png
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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 d7b4372..8788b46 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 ae7eadb..af85ef5 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 6e4551c..aeaa48f 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 0000000..4b208ac
--- /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 0000000..fcc554b
--- /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
+
+
diff --git a/programs/merqury-1.1/util/merylDumpToWig.jar b/programs/merqury-1.1/util/merylDumpToWig.jar
new file mode 100644
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diff --git a/programs/merqury_June2020/util/util.sh b/programs/merqury-1.1/util/util.sh
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diff --git a/programs/merqury_June2020/.DS_Store b/programs/merqury_June2020/.DS_Store
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