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bactopia_sketcher

Tags: taxonomy classification minhash sketch mash sourmash refseq gtdb sample-scope

Create genomic sketches and perform rapid taxonomic classification.

This subworkflow generates MinHash sketches from assembled genomes using Mash and Sourmash. The sketches are compared against reference databases to identify taxonomic classification and find closely related genomes. Mash queries against RefSeq while Sourmash uses the GTDB database for comprehensive taxonomic placement.

Take​

assembly: Channel<Record>
FieldDescription
metaGroovy Record containing sample information
assemblyAssembled contigs in FASTA format
mash_db: Path
sourmash_db: Path
NameTypeDescription
mash_dbPathPath to the Mash RefSeq database for taxonomic classification
sourmash_dbPathPath to the Sourmash GTDB LCA database for taxonomic classification

Emit​

Published​

The sample_outputs and run_outputs emissions are aggregates of output files that will be published in the entry workflow.

sample_outputs​

OutputDescription
sigSourmash signature file
mshMash sketch files for k=21 and k=31
mashMash Screen classification report against RefSeq
sourmashSourmash LCA classification report against GTDB

run_outputs​

No run-scope outputs.

Module Composition​

This subworkflow calls the following modules:

  • bactopia_sketcher - Create genomic sketches and perform rapid taxonomic classification.

Used By​

This subworkflow is used by the following workflows:

  • bactopia - Comprehensive bacterial analysis pipeline for complete genomic characterization.
  • staphopia - Comprehensive analysis pipeline for Staphylococcus aureus isolates.

Citations​

If you use this in your analysis, please cite the following.

Source​

View source on GitHub