Evidence map›Paper›PMID 36469333›Full record

ArticleBioinformatics (Oxford, England)2023

TransFlow: a Snakemake workflow for transmission analysis of Mycobacterium tuberculosis whole-genome sequencing data.

Junhang Pan, Xiangchen Li, Mingwu Zhang, Yewei Lu, Yelei Zhu, Kunyang Wu, Yiwen Wu, Weixin Wang, Bin Chen, Zhengwei Liu and 2 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Bioinformatics (Oxford, England), 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.

0numbers the graph read from it
0cells of the map it votes in
4citing 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

4 citing papers in PubMed.

  1. Article
  2. Article
  3. Review
  4. Article
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

12 authors.

Junhang PanThe Institute of TB Control, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, Zhejiang 310051, China.
Xiangchen LiKey Laboratory of Precision Medicine in Diagnosis and Monitoring Research of Zhejiang Province, Hangzhou, Zhejiang 310020, China.
Mingwu ZhangThe Institute of TB Control, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, Zhejiang 310051, China.
Yewei LuKey Laboratory of Precision Medicine in Diagnosis and Monitoring Research of Zhejiang Province, Hangzhou, Zhejiang 310020, China.
Yelei ZhuThe Institute of TB Control, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, Zhejiang 310051, China.
Kunyang WuThe Institute of TB Control, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, Zhejiang 310051, China.
Yiwen WuDepartment of Medical Oncology, Zhejiang Chinese Medical University, Hangzhou, Zhejiang 310053, China.
Weixin WangKey Laboratory of Precision Medicine in Diagnosis and Monitoring Research of Zhejiang Province, Hangzhou, Zhejiang 310020, China.
Bin ChenThe Institute of TB Control, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, Zhejiang 310051, China.
Zhengwei LiuThe Institute of TB Control, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, Zhejiang 310051, China.
Xiaomeng WangThe Institute of TB Control, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, Zhejiang 310051, China.
Junshun GaoKey Laboratory of Precision Medicine in Diagnosis and Monitoring Research of Zhejiang Province, Hangzhou, Zhejiang 310020, China.ORCID 0000-0001-9040-2289

Funding

Medical Scientific Research Foundation of Zhejiang 2019KY354National and Zhejiang Health Commission Scientific Research Fund WKJ-ZJ-2118
6 · The paper itself

Abstract

motivationWhole-genome sequencing (WGS) is increasingly used to aid the understanding of Mycobacterium tuberculosis (MTB) transmission. The epidemiological analysis of tuberculosis based on the WGS technique requires a diverse collection of bioinformatics tools. Effectively using these analysis tools in a scalable and reproducible way can be challenging, especially for non-experts.

resultsHere, we present TransFlow (Transmission Workflow), a user-friendly, fast, efficient and comprehensive WGS-based transmission analysis pipeline. TransFlow combines some state-of-the-art tools to take transmission analysis from raw sequencing data, through quality control, sequence alignment and variant calling, into downstream transmission clustering, transmission network reconstruction and transmission risk factor inference, together with summary statistics and data visualization in a summary report. TransFlow relies on Snakemake and Conda to resolve dependencies among consecutive processing steps and can be easily adapted to any computation environment. AVAILABILITY AND IMPLEMENTATION: TransFlow is free available at https://github.com/cvn001/transflow. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Indexed as

Mycobacterium tuberculosisTuberculosisHumansSoftwareWhole Genome SequencingWorkflow

Identifiers

PMID36469333
PMCPMC9825751

What OpenQuestion holds

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Registered trials

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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 OpenQuestion graph.