sbx_mapping

A Sunbeam extension for mapping reads against a set of reference genomes.

Config

• genomes_fp: Is the filepath to your reference genomes (in fasta format) all references must have .fasta OR .fa OR .fna extension!!
• samtools_opts: Are the options passed to samtools view
• alnLen: Is the minimum alignment length
• percIdentity: Is the minimum percent identity
• window_size: Is the size of the sliding window for coverage calculations
• sampling: Is the sampling rate for coverage calculations

Docs

More docs.