Description

Downsample long-read sequencing data to the requested coverage using Autocycler.

Input

name:type
description
pattern

meta

:map

Groovy Map containing sample information e.g. [ id:'sample1' ]

reads

:file

Long-read sequencing reads for the sample in FASTQ format (compressed or uncompressed).

*.{fastq,fastq.gz,fq,fq.gz}

genome_size

:integer

Expected genome size in bases used to calculate the target sequencing depth.

Output

name:type
description
pattern

subsampled_reads

meta

:map

Groovy Map containing sample information e.g. [ id:'sample1' ]

$prefix/*.fastq.gz

:file

Subsampled reads produced by Autocycler.

*/*.fastq.gz

versions_autocycler

${task.process}

:string

The name of the process

autocycler

:string

The name of the tool

autocycler --version | sed 's/^[^ ]* //'

:eval

The expression to obtain the version of the tool

Topics

name:type
description
pattern

versions

${task.process}

:string

The name of the process

autocycler

:string

The name of the tool

autocycler --version | sed 's/^[^ ]* //'

:eval

The expression to obtain the version of the tool

Tools

autocycler
GPL-3.0

A tools for generating consensus long-read assemblies for bacterial genomes.

github.com/rrwick/Autocycler/wiki https://github.com/rrwick/Autocycler 10.1093/bioinformatics/btaf474
maintainer
Github user dwells-eit
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