diff --git a/README.md b/README.md
index d6030d604f2e3ba3f13d610a0f3cd7e1a6c37384..b8f7aaaae50a27afc598c7235fc50450bc4e243b 100644
--- a/README.md
+++ b/README.md
@@ -1,6 +1,6 @@
-# REAPRLong : A Tool to Scaffold and Quality Control genome assemblies using (low coverage) long reads
+# REAPRLong: Improvement and QC of genome assemblies using (low coverage) long reads
<p align="center">
-<img src="figures/simple_workflow.pdf">
+<img src="figures/simple_workflow.svg">
</p>
### Dependencies/Prerequisites:
@@ -24,36 +24,11 @@ Otherwise the script can be run using python directly: "python main.py ..."
The help function can be accessed via: ./main.py -h|--help and provides a general overview of how to use and which parameters can be set when using the tool.
REAPRLong needs a genome assembly in fasta format, long reads (e.g. PacBio or ONT) in fastq or fasta format and a path, where output files will be generated, as mandatory input to run. Additional parameters can be set but the default values are tested and generally provide the best results.
REAPRLong can be used as follows:
-\textbf{usage:} main.py [-h] -ge GENOME -fq FASTQ -out OUTDIR [-m MODE] [-t THREADS]
-[-ml MINLINKS] [-mo MINOVERLAP] [-mi MINIDENT] [-it ITERATIONS]
-[-s SIZE] [-fa]
+<p align="center">
+<img src="figures/helpfunction.png">
+</p>
->>optional arguments:
- -h, --help show this help message and exit
- -ge GENOME, --genome GENOME
- Contigs in fasta format
- -fq FASTQ, --fastq FASTQ
- Reads in fastq format
- -out OUTDIR, --outdir OUTDIR
- Directory for output files
- -m MODE, --mode MODE Mode for different types of input data data. Options:
- pb/ont [default=pb]
- -t THREADS, --threads THREADS
- Threads to use(during mapping for now...) [default=4]
- -mo MINOVERLAP, --minoverlap MINOVERLAP
- Minimum overlap needed for two contigs to be merged
- [default=100]
- -mi MINIDENT, --minident MINIDENT
- Minimum identity in overlap needed for two contigs to
- be merged [default=90.0]
- -it ITERATIONS, --iterations ITERATIONS
- maximal iterations performed for breaking set to 0 to
- perfrom NO breaking
- -s SIZE, --size SIZE Size in which the input reads will be split into
- [default=500]
- -fa, --fasta Enable if input reads are in fasta format
-
Example Usage:
./main.py -s 500 -ge /home/max/tests/genome.fasta -fq /home/max/tests/pacbioReads.fastq -out /home/max/tests/output -it 3
@@ -62,18 +37,18 @@ REAPRLong can be used as follows:
REAPRLong generates multiple output files in the specified output directory.
-1. scaffolds.fasta - the generated scaffolds in fasta format
-2. scaffolds.stats - statistics generated for scaffolds.fasta (total basepairs in the assembly, number of scaffolds, longest scaffold, average length and N10/20/30/40/ 50/60/70/80/90/100 values)
-3. scaffolds.gff - gff3 file describing the regions of each new scaffold. Regions can either come from previous contigs or from reads if a gap was filled.
-4. duplicates.fasta - fasta file containing contigs that were fully part of another contig and thus removed from the assembly.
-5. adjusted\_contigs\_it\*.fa - fasta file containing adjusted contigs, if the QC identified misassemblies and broke the previous input. The \* is an integer value indicating the iteration of QC, starting with 0.
-6. coverage\_map\_it\*.gff - a "coverage" map for the input assembly of each iteration. Regions are summarised giving a start and end position and the support given for the region. The support describes the amount of reads mapping continuously in the region substracted by the amount of reads mapping dis-continuously. Negative numbers indicate misassemblies.
-7. deletions\_it\*.txt - identified deletions (within the genome compared to the reads). The \* is an integer value indicating the iteration of QC, starting with 0 which represents the original assembly. Every subsequent number relates to the adjusted\_contigs\_it\*.fa of the previous iteration.
-8. insertions\_it\*.txt - identified insertions (within the genome compared to the reads). The \* is an integer value indicating the iteration of QC, starting with 0 which represents the original assembly. Every subsequent number relates to the adjusted\_contigs\_it\*.fa of the previous iteration.
-9. inversions\_it\*.txt - identified inversions (within the genome compared to the reads). The \* is an integer value indicating the iteration of QC, starting with 0 which represents the original assembly. Every subsequent number relates to the adjusted\_contigs\_it\*.fa of the previous iteration.
-10. misjoins\_it\*.txt - identified misjoins (within the genome compared to the reads). The \* is an integer value indicating the iteration of QC, starting with 0 which represents the original assembly. Every subsequent number relates to the adjusted\_contigs\_it\*.fa of the previous iteration.
+1. **scaffolds.fasta** - the generated scaffolds in fasta format
+2. **scaffolds.stats** - statistics generated for scaffolds.fasta (total basepairs in the assembly, number of scaffolds, longest scaffold, average length and N10/20/30/40/ 50/60/70/80/90/100 values)
+3. **scaffolds.gff** - gff3 file describing the regions of each new scaffold. Regions can either come from previous contigs or from reads if a gap was filled.
+4. **duplicates.fasta** - fasta file containing contigs that were fully part of another contig and thus removed from the assembly.
+5. **adjusted\_contigs\_it\*.fa** - fasta file containing adjusted contigs, if the QC identified misassemblies and broke the previous input. The \* is an integer value indicating the iteration of QC, starting with 0.
+6. **coverage\_map\_it\*.gff** - a "coverage" map for the input assembly of each iteration. Regions are summarised giving a start and end position and the support given for the region. The support describes the amount of reads mapping continuously in the region substracted by the amount of reads mapping dis-continuously. Negative numbers indicate misassemblies.
+7. **deletions\_it\*.txt** - identified deletions (within the genome compared to the reads). The \* is an integer value indicating the iteration of QC, starting with 0 which represents the original assembly. Every subsequent number relates to the adjusted\_contigs\_it\*.fa of the previous iteration.
+8. **insertions\_it\*.txt** - identified insertions (within the genome compared to the reads). The \* is an integer value indicating the iteration of QC, starting with 0 which represents the original assembly. Every subsequent number relates to the adjusted\_contigs\_it\*.fa of the previous iteration.
+9. **inversions\_it\*.txt** - identified inversions (within the genome compared to the reads). The \* is an integer value indicating the iteration of QC, starting with 0 which represents the original assembly. Every subsequent number relates to the adjusted\_contigs\_it\*.fa of the previous iteration.
+10. **misjoins\_it\*.txt** - identified misjoins (within the genome compared to the reads). The \* is an integer value indicating the iteration of QC, starting with 0 which represents the original assembly. Every subsequent number relates to the adjusted\_contigs\_it\*.fa of the previous iteration.
### Workflow
<p align="center">
-<img src="figures/workflow_noOptional.pdf">
+<img src="figures/workflow_noOptional.svg">
</p>