{
  "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.",
  "abstract_shown": true,
  "affiliations": [
    "Department of Health Sciences and Technology, ETH Zurich, 8092 Zurich, Switzerland",
    "Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ 86011, USA",
    "University of Arkansas for Medical Sciences, Department of Biomedical Informatics, Little Rock, AR 72205, USA",
    "Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ 86011, USA; Translational Genomics Research Institute, Flagstaff, AZ 86011, USA",
    "Department of Health Sciences and Technology, ETH Zurich, 8092 Zurich, Switzerland. Electronic address: nicholas.bokulich@hest.ethz.ch"
  ],
  "article_type": null,
  "arxiv": null,
  "author_total": 18,
  "authors": [
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        0
      ],
      "name": "Michał Ziemski",
      "orcid": "0000-0001-6285-8852"
    },
    {
      "affs": [
        0
      ],
      "name": "Liz Gehret"
    },
    {
      "affs": [
        1
      ],
      "name": "Anthony Simard",
      "orcid": "0000-0002-7394-1616"
    },
    {
      "affs": [
        0
      ],
      "name": "Santiago Castro Dau",
      "orcid": "0009-0004-3537-574X"
    },
    {
      "affs": [
        0
      ],
      "name": "Vinzent Risch",
      "orcid": "0009-0002-3904-9218"
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    {
      "affs": [
        0
      ],
      "name": "Doriela Grabocka",
      "orcid": "0009-0005-3731-8199"
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    {
      "affs": [
        0
      ],
      "name": "Christos Konstantinos Matzoros",
      "orcid": "0009-0006-9575-8130"
    },
    {
      "affs": [
        1
      ],
      "name": "Colin Wood",
      "orcid": "0000-0002-8066-3466"
    },
    {
      "affs": [
        0
      ],
      "name": "Paula Momo Cabrera",
      "orcid": "0000-0002-6450-3075"
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    {
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        0
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      "name": "Rodrigo Hernández-Velázquez",
      "orcid": "0009-0009-3048-8573"
    },
    {
      "affs": [
        0
      ],
      "name": "Milo R. Schärer",
      "orcid": "0000-0002-8703-0303"
    },
    {
      "affs": [
        0
      ],
      "name": "Felicia Sandberg"
    },
    {
      "affs": [
        1
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      "name": "Chloe Herman"
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    {
      "affs": [
        1
      ],
      "name": "Keegan Evans"
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    {
      "affs": [
        2
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      "name": "Michael Scott Robeson",
      "orcid": "0000-0001-7119-6301"
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    {
      "affs": [
        0
      ],
      "name": "Evan Bolyen"
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    {
      "affs": [
        3
      ],
      "name": "J. Gregory Caporaso",
      "orcid": "0000-0002-8865-1670"
    },
    {
      "affs": [
        4
      ],
      "name": "Nicholas A. Bokulich",
      "orcid": "0000-0002-1784-8935"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/8dvhqg9h7zmb4.bib",
  "cited_by": 10,
  "doi": "10.1016/j.xgen.2026.101366",
  "fulltext_url": null,
  "id": "8dvhqg9h7zmb4",
  "issns": [
    "2666-979X"
  ],
  "landing_url": "https://doi.org/10.1016/j.xgen.2026.101366",
  "language": "en",
  "licence": "CC-BY",
  "licence_label": "CC BY",
  "licence_source": "journal",
  "licence_url": "https://creativecommons.org/licenses/by/4.0/",
  "metadata_licence": null,
  "native_subjects": [
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      "openalex",
      "1312|Genomics and Phylogenetic Studies"
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  "pdf_url": null,
  "pmcid": "PMC11838374",
  "pmid": "39975011",
  "published": "2026-09-24",
  "publisher": "Elsevier BV",
  "ris": "https://research.draconitic.com/paper/8dvhqg9h7zmb4.ris",
  "sources": [
    {
      "first_seen": "2026-11-04T13:21:07Z",
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      "url": "https://doi.org/10.1016/j.xgen.2026.101366"
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  "subjects": [
    {
      "field": "biochemistry",
      "origin": "openalex:1312|Genomics and Phylogenetic Studies",
      "subfield": "molecular-biology"
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  ],
  "title": "MOSHPIT: Accessible, reproducible metagenome data science on the QIIME 2 framework",
  "title_text": "MOSHPIT: Accessible, reproducible metagenome data science on the QIIME 2 framework",
  "type": "peer-reviewed",
  "updated_at": "2026-11-09T13:21:07Z",
  "url": "https://research.draconitic.com/paper/8dvhqg9h7zmb4",
  "venue": "Cell Genomics",
  "versions": []
}