sourmash

Plugin Overview¶

This QIIME 2 plugin wraps sourmash and supports the calculation and comparison of MinHash signatures.

version: 0.0.0

website: http://sourmash.readthedocs.io/en/latest/

user support:

Please post to the QIIME 2 forum for help with this plugin: https://forum.qiime2.org

citations:

Brown & Irber, 2016; Crusoe et al., 2015

Actions¶

Artifact Classes¶

Formats¶

sourmash compute¶

Computes a sourmash MinHash signature from fasta/q files.

Citations¶

Brown & Irber, 2016; Crusoe et al., 2015

Inputs¶

sequence_file: SampleData[SequencesWithQuality | MAGs]

<no description>[required]

Parameters¶

ksizes: Int

<no description>[required]

scaled: Int

<no description>[required]

track_abundance: Bool

<no description>[default: True]

Outputs¶

min_hash_signature: MinHashSig

<no description>[required]

sourmash compare¶

Compares sourmash signatures and calculates Jacaard distance matrix.

Citations¶

Brown & Irber, 2016; Crusoe et al., 2015

Inputs¶

min_hash_signature: MinHashSig

<no description>[required]

Parameters¶

ksize: Int

<no description>[required]

ignore_abundance: Bool

<no description>[default: True]

Outputs¶

compare_output: DistanceMatrix

<no description>[required]