Version 0.1

README.md

@@ -1,2 +1,77 @@
-# wtdbg2-racon-pilon.pl
-Wrapper for overlap assembly of long reads and polishing
+# wtdbg2-racon-pilon.pl v0.3
+
+## Description
+__Automatic execution of (wtdbg2,) racon and pilon.__
+
+Longread assembly will be executed with wtdbg2.
+Iterative correction with long reads by mapping to the assembly with minimap2 and polishing with Racon.
+Iterative correction with short reads by mapping with either bwa mem or NextGenMap, (merging and) sorting of bam files with samtools and polishing with Pilon.
+
+## Dependencies
+
+`wtdbg2-racon-pilon.pl` will search for the following executables in your `$PATH`:
+
+__Assembly__
+- [wtdbg2](https://github.com/ruanjue/wtdbg2): `wtdbg2`, `wtpoa-cns`
+
+__Long read polishing__
+- [Racon](https://github.com/isovic/racon): `racon`
+- [Minimap2](https://github.com/lh3/minimap2): `minimap2`
+
+__Short read polishing__
+- Java: `java`
+- [bwa (mem)](https://github.com/lh3/bwa): `bwa`
+- [NextGenMap](http://cibiv.github.io/NextGenMap/): `ngm`
+- [samtools](https://github.com/samtools/samtools): `samtools`
+- [Pilon](https://github.com/broadinstitute/pilon): Specify the path to Pilon `jar` file with `-pilon-path`
+
+## Usage
+
+```
+wtdbg2-racon-pilon.pl {-l <longreads.fq> -x <longread tech> | -a <assembly.fa>}
+                      [-p <paired_1.fq>,<paired_2.fq> -u <unpaired.fq>]
+
+Mandatory:
+	-l STR			File containing long reads in fastq format
+	-x STR			Long read sequencing technology for wtdbg2 presets
+				Valid arguments are: rsII, rs, sequel, sq, nanopore, ont,
+				corrected, ccs
+	OR
+	-a STR			File containing an assembly that should be polished in fasta format
+
+Input/pipeline options: [default]
+	-racon-rounds INT	Number of racon iterations [3]
+	-pilon-rounds INT	Number of pilon iterations [3]
+	-pilon-path STR		Complete path to the pilon jar file
+	-sr-mapper STR		Short read mapper for correction with pilon [bwa]
+				Valid arguments are: bwa, ngm
+				To execute different mappers in different pilon rounds supply a
+				comma separated list of mappers. Overrides -pilon-rounds.
+	-p STR			Two files with paired short reads in fastq format comma sperated
+				Can be specified multiple times
+	-u STR			One file with unpaired short reads in fastq format
+				Can be specified multiple times
+	-xmx STR/INT		Maximum java heap size for pilon [current available]
+	-t INT			Number of parallel executed processes [1]
+				Affects wtdbg2, wtpoa-cns, minimap2, racon, bwa mem, ngm,
+				samtools sort and pilon.
+	Pass specific options to tools with:
+	-wtdbg-opts, -wtpoa-opts, -minimap-opts, -racon-opts, -bwa-opts, -ngm-opts, -pilon-opts
+	For example like -wtdbg-opts '-g 100m'
+
+Output options: [default]
+	-o STR			Output directory [.]
+				Will be created if not existing
+	-pre STR		Prefix of output files [{w|<-a>.}r<racon rounds>p<pilon rounds>]
+	-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.
+
+## Known issues
+In some cases Pilon can not polish the assembly with bam files created by NextGenMap.