MTBseq-nf: Enabling Scalable Tuberculosis Genomics "Big Data" Analysis Through a User-Friendly Nextflow Wrapper for MTBseq Pipeline.

Abhinav Sharma, Davi Josué Marcon, Johannes Loubser, Karla Valéria Batista Lima, Gian van der Spuy, Emilyn Costa Conceição

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Article in Microorganisms, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it

0cells of the map it votes in

0citing papers in PubMed

–field-weighted citation impact

1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

0 citing papers in PubMed.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

6 authors.

Abhinav SharmaSAMRC Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town 7505, South Africa.ORCID 0000-0002-6402-6993

Davi Josué MarconPós-Graduação em Biologia Parasitária na Amazônia, Instituto de Ciências Biológicas e da Saúde, Universidade do Estado do Pará, Belém 66095-015, Pará, Brazil.ORCID 0000-0003-1014-422X

Johannes LoubserSAMRC Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town 7505, South Africa.ORCID 0000-0002-2362-0187

Karla Valéria Batista LimaPós-Graduação em Biologia Parasitária na Amazônia, Instituto de Ciências Biológicas e da Saúde, Universidade do Estado do Pará, Belém 66095-015, Pará, Brazil.

Gian van der SpuySAMRC Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town 7505, South Africa.ORCID 0000-0002-9067-5903

Emilyn Costa ConceiçãoSAMRC Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town 7505, South Africa.ORCID 0000-0002-7445-6620

Funding

National Council for Scientific and Technological Development 445784/2023-7National Research Foundation PhD ScholarshipOracle Cloud credits 3083687

6 · The paper itself

Abstract

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

Indexed as

bioinformatics pipelinegenomic surveillanceMTBseqMycobacterium tuberculosisNextflowtuberculosis genomicswhole-genome sequencingworkflow

Identifiers

PMID41471889

DOI10.3390/microorganisms13122685

PMCPMC12734750

What Socratic holds

Textmetadata

LicenceCC BY

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Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the Socratic graph.