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Literature DB >> 33664143

ViroMatch: A Computational Pipeline for the Detection of Viral Sequences from Complex Metagenomic Data.

Abstract

ViroMatch is an automated pipeline that takes metagenomic sequencing reads as input and performs iterative nucleotide and translated nucleotide mapping to identify viral sequences. We provide a Docker image for ViroMatch, so that users will not have to install dependencies.

Entities: Chemical Disease Species

Year: 2021 PMID： 33664143 PMCID： PMC7936641 DOI： 10.1128/MRA.01468-20

Source DB: PubMed Journal: Microbiol Resour Announc ISSN： 2576-098X

19 in total

1. Fast and sensitive protein alignment using DIAMOND.

Authors: Benjamin Buchfink; Chao Xie; Daniel H Huson
Journal: Nat Methods Date: 2014-11-17 Impact factor: 28.547

2. Snakemake--a scalable bioinformatics workflow engine.

Authors: Johannes Köster; Sven Rahmann
Journal: Bioinformatics Date: 2012-08-20 Impact factor: 6.937

Review 3. Human Virome.

Authors: Selene Zárate; Blanca Taboada; Martha Yocupicio-Monroy; Carlos F Arias
Journal: Arch Med Res Date: 2018-02-02 Impact factor: 2.235

4. Association of the eukaryotic vaginal virome with prophylactic antibiotic exposure and reproductive outcomes in a subfertile population undergoing in vitro fertilisation: a prospective exploratory study.

Authors: A M Eskew; M J Stout; B S Bedrick; J K Riley; K R Omurtag; P T Jimenez; R R Odem; V S Ratts; S L Keller; E S Jungheim; K M Wylie
Journal: BJOG Date: 2019-10-20 Impact factor: 6.531

ViroMatch: A Computational Pipeline for the Detection of Viral Sequences from Complex Metagenomic Data.

1. Fast and sensitive protein alignment using DIAMOND.

2. Snakemake--a scalable bioinformatics workflow engine.

Review 3. Human Virome.

4. Association of the eukaryotic vaginal virome with prophylactic antibiotic exposure and reproductive outcomes in a subfertile population undergoing in vitro fertilisation: a prospective exploratory study.

5. Enhanced virome sequencing using targeted sequence capture.

Review 6. The human virome: new tools and concepts.

7. GenBank.

Review 8. Virome genomics: a tool for defining the human virome.

9. Metagenomic analysis of double-stranded DNA viruses in healthy adults.

Review 10. Studying the gut virome in the metagenomic era: challenges and perspectives.

Review 1. Novel technologies to characterize and engineer the microbiome in inflammatory bowel disease.