Description

Computes coverage depth statistics for assembled contigs from one or more fairy sketch files, producing a MetaBAT2-compatible TSV with per-contig mean depth and variance columns.

Input

name:type
description
pattern

meta

:map

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

sketches

:file

One or more fairy sketch files (.bcsp) produced by fairy sketch

*.bcsp

contigs

:file

Assembled contigs in FASTA format

*.{fa,fasta,fna,fa.gz,fasta.gz,fna.gz}

Output

name:type
description
pattern

coverage

meta

:map

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

${prefix}.tsv

:file

MetaBAT2-compatible TSV file with per-contig coverage statistics. Columns: contigName, contigLen, totalAvgDepth, and per-sample mean depth and variance.

*.tsv

versions_fairy

${task.process}

:string

The name of the process

fairy

:string

The name of the tool

fairy --version 2>&1 | sed 's/fairy //'

:eval

The expression to obtain the version of the tool

Topics

name:type
description
pattern

versions

${task.process}

:string

The name of the process

fairy

:string

The name of the tool

fairy --version 2>&1 | sed 's/fairy //'

:eval

The expression to obtain the version of the tool

Tools

fairy
MIT

fairy is a fast, alignment-free, k-mer-based tool for computing coverage depth statistics for metagenomic samples. It is orders of magnitude faster than alignment-based approaches and produces output directly compatible with MetaBAT2.

github.com/bluenote-1577/fairy
maintainer
Github user vagkaratzas
get in touch
Ask a question on Slack Open an issue on GitHub