A nextflow workflow for detection of microbial genomes from cancer whole-genome-sequenced bams.

The micrite pipeline is made up of three sub-pipelines

1. micrite-screen for rapid screening of BAMs for microbial reads.
2. micrite-sleuth for slower but exhaustive in silico validation that a specific species of interest (e.g. those flagged by micrite-screen) is indeed present and not just misclassified host-sequences.
3. micrite-subtype for deep genotyping of common oncoviruses (in-development).

To get started with micrite we recommend running micrite-screen as described here.