Bactopia Pipelines

Bactopia Pipelines are complete analysis pipelines built from Bactopia's subworkflows and modules. There are 3 pipelines available.

Pipeline	Description
cleanyerreads	Quality control and optional host read removal from raw sequencing reads.
staphopia	Comprehensive analysis pipeline for Staphylococcus aureus isolates.
teton	Taxonomic classification and abundance profiling of metagenomic reads.