Software and Resources

QIIME 2 is a microbiome multi-omics bioinformatics and data science platform that is trusted, free, open source, extensible, and community developed and supported.

Website: external page https://qiime2.org/

Publication: external page https://doi.org/10.1038/s41587-019-0209-9

MOSHPIT is a comprehensive toolkit of plugins for whole metagenome assembly, annotation, and analysis built on the microbiome multi-omics data science framework QIIME 2. MOSHPIT enables flexible, modular, fully reproducible workflows for read-based or assembly-based analysis of metagenome data.

Website: external page https://moshpit.readthedocs.io/

Publication: external page https://doi.org/10.1101/2025.01.27.635007

RESCRIPt is a python 3 package to support a variety of operations for managing and curating reference sequence databases, DNA/RNA sequence data, and taxonomic data, built on the QIIME 2 framework for fully reproducible, provenance-tracked reference database curation and management.

Website: external page https://github.com/bokulich-lab/RESCRIPt/

Publication: external page https://doi.org/10.1371/journal.pcbi.1009581

q2-fondue (Functions for reproducibly Obtaining and Normalizing Data re-Used from Elsewhere) is a QIIME 2 plugin for programmatic access to sequences and metadata from NCBI Sequence Read Archive (SRA). It enables user-friendly acquisition, re-use, and management of public nucleotide sequence (meta)data while adhering to open data principles. 

Website: external page https://github.com/bokulich-lab/q2-fondue

Publication: external page https://doi.org/10.1093/bioinformatics/btac639

FermDB is an open database and dashboard of information about global fermented foods. This comprises the largest manually curated database of fermented food information, classified according to source and substrate origin.

Website: external page https://bokulich-lab.github.io/FermDB/

Publication: external page https://doi.org/10.1016/j.tifs.2024.104569