Commit 0740ace6 authored by Raphael Müller's avatar Raphael Müller
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Update README.md

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......@@ -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.
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