Description

Annotate list of metagenome members (based on sourmash signature matches) with taxonomic information.

Input

name:type
description
pattern

meta{:bash}

:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

gather_results{:bash}

:file

Mandatory table with signatures classified as belonging to any of the genomes in the sourmash database(s), result of sourmash gather command.

taxonomy{:bash}

:file

One or more databases with lineages (in CSV format, Mandatory)

Output

name:type
description
pattern

result{:bash}

meta{:bash}

:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

*.with-lineages.csv.gz{:bash}

:file

Table with signatures classified as belonging to any of the genomes in the sourmash database(s) with an additional ‘lineage’ column containing the taxonomic information for each database match.

*{csv.gz}

versions{:bash}

versions.yml{:bash}

:file

File containing software versions

versions.yml

Tools

sourmash
BSD-3-clause

Compute and compare FracMinHash signatures for DNA data sets.

sourmash.readthedocs.io https://github.com/sourmash-bio/sourmash 10.21105/joss.00027
maintainers
Github user vmikk
Github user taylorreiter
get in touch
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