Version v1.1.0

What's Changed

• Fix linting problems. by @mberacochea in #2
• Dram fixes by @Ales-ibt in #3
• PR to update optimised params and remove bams after bwamem alignment by @Ales-ibt in #4
• Fix a string comparison that was causing the pipeline to crash. by @mberacochea in #5

Added support for the human-gut-v2-0-2 biome.

Full Changelog: v1.0.0...v1.1.0

Shallow-mapping pipeline v1.0.0

This release of the pipeline can be run with the following biomes:

• chicken-gut-v1-0-1
• mouse-gut-v1-0

Other biomes can be supported under request by raising an issue in this repo.

Sourmash is the default tool to generate taxonomic profiles. Optionally, bwamem2 can be used as well.
Pangenome function tables are used by default to generate functional profiles. Core functions can be used as well.

Databases are downloaded using the bash script provided. MGnify hosts all DBs needed, so the user doesn't need to generate them from scratch.