دورية أكاديمية
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hgtseq: A Standard Pipeline to Study Horizontal Gene Transfer.

التفاصيل البيبلوغرافية
العنوان: hgtseq: A Standard Pipeline to Study Horizontal Gene Transfer.
المؤلفون: Carpanzano S; Department of Biology and Biotechnology, University of Pavia, 27100 Pavia, Italy., Santorsola M; Department of Biology and Biotechnology, University of Pavia, 27100 Pavia, Italy., Nf-Core Community; Department of Biology and Biotechnology, University of Pavia, 27100 Pavia, Italy., Lescai F; Department of Biology and Biotechnology, University of Pavia, 27100 Pavia, Italy.
المصدر: International journal of molecular sciences [Int J Mol Sci] 2022 Nov 22; Vol. 23 (23). Date of Electronic Publication: 2022 Nov 22.
نوع المنشور: Journal Article
اللغة: English
بيانات الدورية: Publisher: MDPI Country of Publication: Switzerland NLM ID: 101092791 Publication Model: Electronic Cited Medium: Internet ISSN: 1422-0067 (Electronic) Linking ISSN: 14220067 NLM ISO Abbreviation: Int J Mol Sci Subsets: MEDLINE
أسماء مطبوعة: Original Publication: Basel, Switzerland : MDPI, [2000-
مواضيع طبية MeSH: Gene Transfer, Horizontal* , Evolution, Molecular*, Animals ; Humans ; Prokaryotic Cells ; Bacteria/genetics ; Base Sequence ; Phylogeny ; Mammals/genetics
مستخلص: Horizontal gene transfer (HGT) is well described in prokaryotes: it plays a crucial role in evolution, and has functional consequences in insects and plants. However, less is known about HGT in humans. Studies have reported bacterial integrations in cancer patients, and microbial sequences have been detected in data from well-known human sequencing projects. Few of the existing tools for investigating HGT are highly automated. Thanks to the adoption of Nextflow for life sciences workflows, and to the standards and best practices curated by communities such as nf-core, fully automated, portable, and scalable pipelines can now be developed. Here we present nf-core/hgtseq to facilitate the analysis of HGT from sequencing data in different organisms. We showcase its performance by analysing six exome datasets from five mammals. Hgtseq can be run seamlessly in any computing environment and accepts data generated by existing exome and whole-genome sequencing projects; this will enable researchers to expand their analyses into this area. Fundamental questions are still open about the mechanisms and the extent or role of horizontal gene transfer: by releasing hgtseq we provide a standardised tool which will enable a systematic investigation of this phenomenon, thus paving the way for a better understanding of HGT.
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معلومات مُعتمدة: FRG - Fondo Ricerca & Giovani University of Pavia
فهرسة مساهمة: Keywords: bioinformatic pipelines; exome; horizontal gene transfer; microbiome; sequencing
تواريخ الأحداث: Date Created: 20221211 Date Completed: 20221216 Latest Revision: 20221221
رمز التحديث: 20231215
مُعرف محوري في PubMed: PMC9738810
DOI: 10.3390/ijms232314512
PMID: 36498841
قاعدة البيانات: MEDLINE
الوصف
تدمد:1422-0067
DOI:10.3390/ijms232314512