Open access
MOSHPIT: Accessible, reproducible metagenome data science on the QIIME 2 framework.
M. Ziemski
Liz Gehret
Anthony Simard
Santiago Castro Dau
Vinzent Risch
D. Grabocka
Christos Matzoros
Colin Wood
Paula Momo Cabrera
Rodrigo Hernández-Velázquez
Milo R. Schärer
Felicia Sandberg
Chloe Herman
Keegan Evans
Michael S. Robeson
Evan Bolyen
J. Caporaso
N. Bokulich
Medicine
Abstract
Metagenome sequencing has revolutionized functional microbiome analysis across diverse ecosystems but is fraught with technical hurdles. We introduce MOSHPIT (MOdular SHotgun metagenome Pipelines with Integrated provenance Tracking; https://moshpit.qiime2.org)-software built on the QIIME 2/rachis framework (Q2F) that integrates best-in-class CAMI II- and LEMMI-validated metagenome tools with robust provenance tracking and multiple user interfaces-enabling streamlined, reproducible metagenome analysis for all expertise levels. By building on Q2F, MOSHPIT enhances scalability, interoperability, and reproducibility in complex workflows, democratizing and accelerating discovery at the frontiers of metagenomics.