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Updated: Sep 26, 2026

Microbiota Analysis Using Two-step PCR and Next-generation 16S rRNA Gene Sequencing
Published on: October 15, 2019
MOSHPIT: Accessible, reproducible metagenome data science on the QIIME 2 framework
Michal Ziemski1, Liz Gehret1, Anthony Simard2
1Department of Health Sciences and Technology, ETH Zurich, 8092 Zurich, Switzerland.
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.
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