Description

A submodule that clusters the merged AMP hits generated from ampcombi2/parsetables and ampcombi2/complete using MMseqs2 cluster.

Input

name:type
description
pattern

summary_file:file

A file corresponding to the Ampcombi_summary.tsv that is generated by running ‘ampcombi complete’. It is a file containing all the merged AMP results from all samples and all tools.

*.tsv

Output

name:type
description
pattern

cluster_tsv

Ampcombi_summary_cluster.tsv:file

A file containing all the results from the merged input table ‘Ampcombi_summary.tsv’, but also including the cluster id number. The clustering is done using MMseqs2 cluster.

*.tsv

rep_cluster_tsv

Ampcombi_summary_cluster_representative_seq.tsv:file

A file containing the representative sequences of the clusters estimated by the tool. The clustering is done using MMseqs2 cluster.

*.tsv

log

Ampcombi_cluster.log:file

A log file that captures the standard output for the entire process in a log file. Can be activated by --log.

*.log

versions

versions.yml:file

File containing software versions

versions.yml

Tools

ampcombi2/cluster
MIT

A tool for clustering all AMP hits found across many samples and supporting many AMP prediction tools.

github.com/Darcy220606/AMPcombi https://github.com/Darcy220606/AMPcombi/tree/dev
included in
funcscan
maintainer
Github user darcy220606
get in touch
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