BIOM tools

These are a set of scripts used to manipulate BIOM (http://biom-format.org/) files.

REQUIREMENTS: Python v3, biom, numpy and h5py packages.

Modifying BIOM files

• biom_add_metadata.py - Add metadata to a BIOM file
• change_biom_ids.py - Convert IDs in a BIOM.
• change_biom_table.py - Change table type of a BIOM file.
• copy_biom_md.py - Copy metadata from one BIOM file to another.
• filter_biom.py - Filter a BIOM file.
• merge_biom.py - Merge OTU tables.
• single_rarefaction.py - Rarefy/subsample a BIOM file.
• sort_biom.py - Sort a BIOM file.
• split_biom.py - Split a BIOM file using the metadata.
• summarize_biom.py - Summarize a BIOM file.

BIOM converstion

• biom2gmt.py - Convert a BIOM metadata to GMT file
• biom2txt.py - Convert a BIOM file to text table.

Create BIOM files

• kraken2biom.py - Convert Kraken2 report(s) to a BIOM.
• uclust2biom.py - Create BIOM file from UCLUST output table.