Summary: 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.
We asked a global cohort of authors and reviewers of manuscripts published in the past 5 years at Cell Genomics to tell us about their specific research. We then asked them to reflect upon the current state of their respective field and what they foresee or would like to see changing and growing over the next 5 years.
