sbx_shotgun_unifrac is a sunbeam extension for assigning shotgun reads to a bacterial tree of life and performing population statistics like UniFrac. This pipeline uses bwa for initial alignment steps and QIIME2 with the GreenGenes plugin for the reference phylogeny and performing the core methods.
- threads: Number of threads to use with
bwa - wolr_fp: Directory with WoLr2 bowtie2 database
- tree_fp: Qiime2 phylogeny
- woltka_map_fp: Path to the directory containing the Woltka map file
More docs.