Update README.md

README.md

@@ -133,81 +133,6 @@ R scripts have been improved and rewritten
 
 https://github.com/schellt/backmap
 
-## backmap.pl v0.3
-
-### Description
-__Automatic read mapping and genome size estimation from coverage.__
-
-Automatic mapping of paired, unpaired, PacBio and Nanopore reads to an assembly with `bwa mem` or `minimap2`, execution of `qualimap bamqc` and estimation of genome size from mapped nucleotides divided by mode of the coverage distribution (>0). This method was first pulished in Schell et al. (2017) and is slightly refined in this script.  
-The tools `samtools`, `bwa` and/or `minimap2` need to be in your `$PATH`. The tools `qualimap`, `multiqc`, `bedtools` and `Rscript` are optional but needed to create the mapping quality report, coverage histogram as well as genome size estimation and to plot of the coverage distribution respectively.
-
-### Dependencies
-
-`backmap.pl` needs the following perl modules and will search for executables in your `$PATH`:
-
-Mandatory:
-- [Number::FormatEng](https://metacpan.org/pod/Number::FormatEng)
-- [Parallel::Loops](https://metacpan.org/pod/Parallel::Loops)
-- [samtools](https://github.com/samtools/samtools): `samtools`
-
-Short read mapping:
-- [bwa (mem)](https://github.com/lh3/bwa): `bwa`
-
-Long read mapping:
-- [minimap2](https://github.com/lh3/minimap2): `minimap2`
-
-Optional:
-- [Qualimap](http://qualimap.bioinfo.cipf.es/): `qualimap`
-- [MultiQC](https://multiqc.info/): `multiqc`
-- [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>} |
-            -pb <pacbio.fq> | -ont <ont.fq> } | -b <mapping.bam>]
-
-Mandatory:
-	-a STR		Assembly were reads should mapped to in fasta format
-	AND AT LEAST ONE OF
-	-p STR		Two files with paired Illumina reads comma sperated
-	-u STR		Fastq file with unpaired Illumina reads
-	-pb STR		Fasta or fastq file with PacBio reads
-	-ont STR	Fasta or fastq file with Nanopore reads
-	OR
-	-b STR		Bam file to calculate coverage from
-			Skips read mapping
-			Overrides -nh
-			Technologies will recognized correctly if filenames end with
-			.pb(.sort).bam or .ont(.sort).bam for PacBio and Nanopore respectively.
-			Otherwise they are assumed to be from Illumina.
-			
-	All mandatory options except of -a can be specified multiple times
-
-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 if -a is used [filename of -a]
-	-sort		Sort the bam file(s) (-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]
-	-mo STR		Options passed to minimap [PacBio: -H -x map-pb; ONT: -x map-ont]
-	-qo STR		Options passed to qualimap [none]
-	Pass options with quotes e.g. -bo "<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
 Schell T, Feldmeyer B, Schmidt H, Greshake B, Tills O et al. (2017). An Annotated Draft Genome for _Radix auricularia_ (Gastropoda, Mollusca). _Genome Biology and Evolution_, 9(3):585–592, <https://doi.org/10.1093/gbe/evx032>
 
@@ -228,7 +153,6 @@ Quinlan AR, Hall IM (2010). BEDTools: a flexible suite of utilities for comparin
 - Rscript:  
 R Core Team (2019). R: A Language and Environment for Statistical Computing. <http://www.R-project.org/>
 
-
 # testdata
 
 There are no Nanopore reads.