This work introduces MOSHPIT (MOdular SHotgun metagenome Pipelines with Integrated provenance Tracking), 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.
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.
Metaproteomic analyses commonly rely on protein sequence databases, yet database construction remains one of the most variable steps in metaproteomic workflows. Here, I present MetaproDB, a flexible and reproducible framework for biome-informed protein-sequence-database construction in metaproteomics. MetaproDB integ...
M. Arıkan· Journal of Proteome Research· 0 citations
Meta2Data is a modular, largely automated pipeline implemented in Python and Bash for the retrieval, standardization, and processing of public microbiome sequencing data. It retrieves metadata from major public repositories, including INSDC and CNCB, using user-provided keywords or BioProject/BioSample identifiers. Ret...
Jia-Xuan Li, Anne Duplouy, Lin-Yang Sun· bioRxiv· 0 citations
This work presents a novel, integrative framework that connects strategic omics and sequencing technologies to combine sophisticated metagenomics studies with customized next-generation sequencing techniques to lay the groundwork for next-generation ecological predictions and precise microbiome engineering with proper...
P. Kumari, Gaurav Sharma, M. Gupta et al.· Chemical biology letters· 0 citations
metaKEGG is a comprehensive software package designed to streamline the visualization and integration of pathway enrichment results from multi-omics data, providing accessible and detailed insights into the molecular mechanisms driving health and disease. Unlike standard pipeline approaches, metaKEGG incorporates novel...
Michalis Lazaratos, N. Haacke, J. Gaugel et al.· Biochemistry and Biophysics...· 0 citations
This perspective highlights recent advances in multi-omics microbiome research, outlines key obstacles in data integration and metadata harmonization, and proposes a collaborative roadmap for scalable, FAIR-compliant multi-omics investigations and potentially disruptive Artificial Intelligence advances.
T. Van Den Bossche, Eunice Lazau, Velma T. E. Aho et al.· Nature Communications· 0 citations
The results establish Sma3s v3 as a scalable and interpretable tool for functional annotation and re-annotation of proteomes, pangenomes, and metagenomic protein catalogues.
Alejandro Rubio, Jesús L. García-Junco Alcalá, Elisa Luque-Jiménez et al.· bioRxiv· 0 citations
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