Databases

Modules

Mouse Removal Database

The CAP uses mm39 for mouse removal. The raw (fasta) genome is indexed using Bowtie2.

class cap2.pipeline.databases.MouseRemovalDB(*args, **kwargs)

This class is responsible for building and/or retriveing validating the database which will be used to remove mouse reads from the sample.

Human Removal Database

The CAP uses Hg38 with alternate contigs. for human removal. The raw (fasta) genome is indexed using Bowtie2. Th rationale for picking this genome is based on this.

class cap2.pipeline.databases.HumanRemovalDB(*args, **kwargs)

This class is responsible for building and/or retriveing validating the database which will be used to remove human reads from the sample.

Kraken2 Taxonomic Databases

The CAP uses built in tools from Kraken2 to build a databse. The CAP2 taxonomic databases includes archaea, bacteria, plasmids, viruses, fungi, protozoa, and human.

class cap2.pipeline.databases.Kraken2DB(*args, **kwargs)