Description

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

Input

name:type
description
pattern

meta{:bash}

:map

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

reads{:bash}

:file

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

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

genome_size{:bash}

:integer

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

Output

name:type
description
pattern

subsampled_reads{:bash}

meta{:bash}

:map

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

$prefix/*.fastq.gz{:bash}

:file

Subsampled reads produced by Autocycler.

*/*.fastq.gz

versions_autocycler{:bash}

${task.process}{:bash}

:string

The name of the process

autocycler{:bash}

:string

The name of the tool

autocycler --version | sed 's/^[^ ]* //'{:bash}

:eval

The expression to obtain the version of the tool

Topics

name:type
description
pattern

versions{:bash}

${task.process}{:bash}

:string

The name of the process

autocycler{:bash}

:string

The name of the tool

autocycler --version | sed 's/^[^ ]* //'{:bash}

: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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