Description

Compare many FracMinHash signatures generated by sourmash sketch.

Input

Name (Type)
Description
Pattern

meta (map)

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

]

signatures (file)

Files containing signatures (hash sketches) of samples

*.{sig}

file_list (file)

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

save_numpy_matrix (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 (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

meta (map)

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

]

versions (file)

File containing software versions

versions.yml

matrix (file)

An optional (dis)similarity matrix numpy binary format

*.comp

csv (file)

An optional (dis)similarity matrix in CSV format

*.comp.csv

labels (file)

A text file that specifies the labels in the output numpy_matrix

*.comp.labels.txt
included in
pathogensurveillance
maintainer
Github user taylorreiter
get in touch
Ask a question on Slack Open an issue on GitHub

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