Description

Search a metagenome sourmash signature against one or many reference databases and return the minimum set of genomes that contain the k-mers in the metagenome.

Input

name:type
description
pattern

meta{:bash}

:map

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

signature{:bash}

:file

File containing signatures (hash sketches) of a sample

*.{sig}

database{:bash}

:file

database

save_unassigned{:bash}

:boolean

If true, output will contain a file that is a sourmash signature containing the unassigned hashes from the query

save_matches_sig{:bash}

:boolean

If true, output will contain a file that is a sourmash signature composed of the FracMinHash sketches that were matched in the database and that matched the query

save_prefetch{:bash}

:boolean

If true, output will contain a file with all prefetch-matched signatures from the database

save_prefetch_csv{:bash}

:boolean

If true, output will contain a csv file with the names of all prefetch-matched signatures

Output

name:type
description
pattern

result{:bash}

meta{:bash}

:map

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

*.csv.gz{:bash}

:file

Table with signatures classified as belonging to any of the genomes in the sourmash database(s).

*{csv.gz}

unassigned{:bash}

meta{:bash}

:map

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

*_unassigned.sig.zip{:bash}

:file

A FracMinHash sketch containing hashes (k-mers) that did not match to any of the genomes in the sourmash database(s).

*{sig.zip}

matches{:bash}

meta{:bash}

:map

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

*_matches.sig.zip{:bash}

:file

A signature containing FracMinHash sketches of genomes in the sourmash database.

*{sig.zip}

prefetch{:bash}

meta{:bash}

:map

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

*_prefetch.sig.zip{:bash}

:file

All prefetch-matched signatures from the database.

*{sig.zip}

prefetchcsv{:bash}

meta{:bash}

:map

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

*_prefetch.csv.gz{:bash}

:file

The names of all prefetch-matched signatures from the database in CSV format.

*{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
included in
magmap
maintainers
Github user vmikk
Github user taylorreiter
get in touch
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