Commit 0740ace6 authored by Raphael Müller's avatar Raphael Müller
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parent f3768014
......@@ -133,81 +133,6 @@ R scripts have been improved and rewritten
## 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 `$PATH`. The tools `qualimap`, `multiqc`, `bedtools` and `Rscript` are optional but needed to create the mapping quality report, coverage histogram as well as genome size estimation and to plot of the coverage distribution respectively.
### Dependencies
`` needs the following perl modules and will search for executables in your `$PATH`:
- [Number::FormatEng](
- [Parallel::Loops](
- [samtools]( `samtools`
Short read mapping:
- [bwa (mem)]( `bwa`
Long read mapping:
- [minimap2]( `minimap2`
- [Qualimap]( `qualimap`
- [MultiQC]( `multiqc`
- [bedtools]( `bedtools`
- [Rscript]( `Rscript`
### Usage
``` [-a <assembly.fa> {-p <paired_1.fq>,<paired_2.fq> | -u <unpaired.fq>} |
-pb <pacbio.fq> | -ont <ont.fq> } | -b <mapping.bam>]
-a STR Assembly were reads should mapped to in fasta format
-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
-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, <>
......@@ -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. <>
# testdata
There are no Nanopore reads.
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