Work

MOSHPIT: Accessible, reproducible metagenome data science on the QIIME 2 framework

Year: 2026

Type: article

Abstract: Metagenome sequencing has revolutionized functional microbiome analysis across diverse ecosystems, but is fraught with technical hurdles. We introduce MOSHPIT (https://moshpit.readthedocs.io), software built on the QIIME 2 framework (Q2F) that integrates best-in-class CAMI2-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.

Source: Cell Genomics

DOI: 10.1016/j.xgen.2026.101366

Authors: Michal Ziemski, Liz Gehret, Anthony Simard, Santiago Castro Dau, Vinzent Risch, Doriela 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. Gregory Caporaso, Nicholas A. Bokulich

Institutions: ETH Zurich, Northern Arizona University, University of Arkansas for Medical Sciences, Translational Genomics Research Institute

Language: English

Topic: Genomics and Phylogenetic Studies

Subfield: Molecular Biology

Field: Biochemistry, Genetics and Molecular Biology

Domain: Life Sciences

Open Access status: gold

Estimated APC paid: $8,900

Funders: Silicon Valley Community Foundation, Chan Zuckerberg Initiative, Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung, Board of the Swiss Federal Institutes of Technology, National Institutes of Health, National Cancer Institute

Awards: Advanced Development of Informatics Technologies for Cancer Research and Management (U24 Clinical Trial Optional), G7714909483

OpenAlex ID: W7214196201

FWCI: 10.22

Cites: 42

Cited by: 10

Related to: 10