Description

Compare many FracMinHash signatures generated by sourmash sketch.

Input

name:type
description
pattern

meta{:bash}

:map

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

signatures{:bash}

:file

Files containing signatures (hash sketches) of samples

*.{sig}

file_list{:bash}

:file

An optional file specifying a list of file paths that should be appended to the input signatures.

save_numpy_matrix{:bash}

:boolean

If true, output will contain a (dis)similarity matrix numpy binary format. At least one of save_numpy_matrix or save_csv is required.

save_csv{:bash}

:boolean

If true, output will contain a (dis)similarity matrix in CSV format At least one of save_numpy_matrix or save_csv is required.

Output

name:type
description
pattern

matrix{:bash}

meta{:bash}

:map

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

*comp.npy{:bash}

:file

An optional (dis)similarity matrix numpy binary format

*.comp

labels{:bash}

meta{:bash}

:map

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

*comp.npy.labels.txt{:bash}

:file

A text file that specifies the labels in the output numpy_matrix

*.comp.labels.txt

csv{:bash}

meta{:bash}

:map

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

*comp.csv{:bash}

:file

An optional (dis)similarity matrix in CSV format

*.comp.csv

versions{:bash}

versions.yml{:bash}

:file

File containing software versions

versions.yml

Tools

sourmash
BSD-3-clause

Compute and compare FracMinHash signatures for DNA and protein data sets.

sourmash.readthedocs.io https://github.com/sourmash-bio/sourmash 10.21105/joss.00027
included in
pathogensurveillance
maintainer
Github user taylorreiter
get in touch
Ask a question on Slack Open an issue on GitHub