Version 0.1

Author: schellt

README.md

@@ -1,2 +1,63 @@
-# backmap
-Wrapper for short read mapping, creation of quality report and estimation of genome size
+# backmap.pl v0.1
+
+## Description
+__Automatic short read mapping and genome size estimate from coverage.__
+
+Automatic mapping of paired and unpaired reads to an assembly with `bwa mem`, execution of `qualimap bamqc` and estimation of genome size from mapped nucleotides divided by mode (>0).
+The tools `bwa` and `samtools` need to be in your `$PATH`. The tools `qualimap`, `bedtools` and `Rscript` are optional but needed to create the mapping quality report, coverage histogram and plot of the coverage distribution respectively.
+
+## Dependencies
+
+`backmap.pl` will search for the following executables in your `$PATH`:
+
+Mandatory:
+- [bwa (mem)](https://github.com/lh3/bwa): `bwa`
+- [samtools](https://github.com/samtools/samtools): `samtools` 
+
+Optional:
+- [Qaulimap](http://qualimap.bioinfo.cipf.es/): `qualimap`
+- [bedtools](https://bedtools.readthedocs.io/en/latest/) `bedtools`
+- [Rscript](https://www.r-project.org/) `Rscript`
+
+## Usage
+
+```
+backmap.pl [-a <assembly.fa> {-p <paired_1.fq>,<paired_2.fq> | -u <unpaired.fq>} |
+            -b <mapping.bam>]
+
+Mandatory:
+	-a STR		Assembly were reads should mapped to in fasta format
+	-p STR		Two files with paired reads comma sperated
+			Can be specified multiple times
+	-u STR		One file with unpaired reads
+			Can be specified multiple times
+	OR
+	-b STR		Bam file to calculate coverage from
+			Skips read mapping
+			Overrides -nh and -ne
+
+Options: [default]
+	-o STR		Output directory [.]
+			Will be created if not existing
+	-t INT		Number of parallel executed processes [1]
+			Affects bwa mem, samtools sort, qualimap bamqc
+	-pre STR	Prefix of output files [filename of -a or -b]
+	-sort		Sort the bam file (-b) [off]
+	-nq		Do not run qualimap bamqc [off]
+	-nh		Do not create coverage histogram [off]
+			Implies -ne
+	-ne		Do not estimate genome size [off]
+	-kt		Keep temporary bam files [off]
+	-bo STR		Options passed to bwa [-a -c 10000]
+			Pass options with -bo "<options>"
+	-qo STR		Options passed to qualimap [none]
+			Pass options with -qo "<options>"
+	-v		Print executed commands to STDERR [off]
+	-dry-run	Only print commands to STDERR instead of executing [off]
+
+	-h or -help	Print this help and exit
+	-version	Print version number and exit
+```
+
+## Citation
+If you use this tool please cite the dependencies.