{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,27]],"date-time":"2025-11-27T05:36:04Z","timestamp":1764221764672,"version":"3.46.0"},"reference-count":30,"publisher":"MDPI AG","issue":"12","license":[{"start":{"date-parts":[[2025,11,25]],"date-time":"2025-11-25T00:00:00Z","timestamp":1764028800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Microorganisms"],"abstract":"<jats:p>The MTBseq pipeline, published in 2018, was designed to address bioinformatics challenges in tuberculosis (TB) research using whole-genome sequencing (WGS) data. It was the first publicly available tool on GitHub to perform full analysis of WGS data for Mycobacterium tuberculosis complex (MTBC) encompassing quality control through mapping, variant calling for lineage classification, drug resistance prediction, and phylogenetic inference. However, the pipeline\u2019s architecture is not optimal for analyses on high-performance computing or cloud computing environments that often involve large datasets. To overcome this limitation, we developed MTBseq-nf, a Nextflow wrapper that provides parallelization for faster execution speeds in addition to several other significant enhancements. The MTBseq-nf wrapper can run several instances of the same step in parallel, fully utilizing the available resources, unlike the linear, batched analysis of samples in the TBfull step of the MTBseq pipeline. For evaluation of scalability and reproducibility, we used 90 M. tuberculosis genomes (European Nucleotide Archive\u2014ENA accession PRJEB7727) for the benchmarking analysis on a dedicated computational server. In our benchmarks, MTBseq-nf in its parallel mode is at least twice as fast as the standard MTBseq pipeline for cohorts exceeding 20 samples. Through integration with the best practices of nf-core, Bioconda, and Biocontainers projects MTBseq-nf ensures reproducibility and platform independence, providing a scalable and efficient solution for TB genomic surveillance.<\/jats:p>","DOI":"10.3390\/microorganisms13122685","type":"journal-article","created":{"date-parts":[[2025,11,25]],"date-time":"2025-11-25T15:29:47Z","timestamp":1764084587000},"page":"2685","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["MTBseq-nf: Enabling Scalable Tuberculosis Genomics \u201cBig Data\u201d Analysis Through a User-Friendly Nextflow Wrapper for MTBseq Pipeline"],"prefix":"10.3390","volume":"13","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-6402-6993","authenticated-orcid":false,"given":"Abhinav","family":"Sharma","sequence":"first","affiliation":[{"name":"SAMRC Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town 7505, South Africa"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1014-422X","authenticated-orcid":false,"given":"Davi Josu\u00e9","family":"Marcon","sequence":"additional","affiliation":[{"name":"P\u00f3s-Gradua\u00e7\u00e3o em Biologia Parasit\u00e1ria na Amaz\u00f4nia, Instituto de Ci\u00eancias Biol\u00f3gicas e da Sa\u00fade, Universidade do Estado do Par\u00e1, Bel\u00e9m 66095-015, Par\u00e1, Brazil"},{"name":"Se\u00e7\u00e3o de Bacteriologia e Micologia, Instituto Evandro Chagas, Ananindeua 67030-000, Par\u00e1, Brazil"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2362-0187","authenticated-orcid":false,"given":"Johannes","family":"Loubser","sequence":"additional","affiliation":[{"name":"SAMRC Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town 7505, South Africa"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Karla Val\u00e9ria Batista","family":"Lima","sequence":"additional","affiliation":[{"name":"P\u00f3s-Gradua\u00e7\u00e3o em Biologia Parasit\u00e1ria na Amaz\u00f4nia, Instituto de Ci\u00eancias Biol\u00f3gicas e da Sa\u00fade, Universidade do Estado do Par\u00e1, Bel\u00e9m 66095-015, Par\u00e1, Brazil"},{"name":"Se\u00e7\u00e3o de Bacteriologia e Micologia, Instituto Evandro Chagas, Ananindeua 67030-000, Par\u00e1, Brazil"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9067-5903","authenticated-orcid":false,"given":"Gian","family":"van der Spuy","sequence":"additional","affiliation":[{"name":"SAMRC Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town 7505, South Africa"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7445-6620","authenticated-orcid":false,"given":"Emilyn Costa","family":"Concei\u00e7\u00e3o","sequence":"additional","affiliation":[{"name":"SAMRC Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town 7505, South Africa"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2025,11,25]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"235","DOI":"10.1038\/s41576-022-00551-z","article-title":"Navigating Bottlenecks and Trade-Offs in Genomic Data Analysis","volume":"24","author":"Berger","year":"2023","journal-title":"Nat. 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