ASPICov: An automated pipeline for identification of SARS-Cov2 nucleotidic variants

Type Article
Date 2022-01
Language English
Author(s) Tilloy ValentinORCID1, Cuzin Pierre2, Leroi LauraORCID2, Guérin Emilie3, Durand PatrickORCID2, Alain SophieORCID1
Affiliation(s) 1 : Centre National de Référence des Herpèsvirus, CHU Dupuytren, Limoges, France, UF9481 Bioinformatique, CHU Dupuytren, Limoges, France, UF8843 Génomique médicale, CHU Dupuytren, Limoges, France
2 : IFREMER-IRSI-Service de Bioinformatique, Centre Bretagne, Plouzane, France
3 : UF8843 Génomique médicale, CHU Dupuytren, Limoges, France
Source Plos One (1932-6203) (Public Library of Science (PLoS)), 2022-01 , Vol. 17 , N. 1 , P. e0262953 (5p.)
DOI 10.1371/journal.pone.0262953
WOS© Times Cited 5
Abstract

ASPICov was developed to provide a rapid, reliable and complete analysis of NGS SARS-Cov2 samples to the biologist. This broad application tool allows to process samples from either capture or amplicon strategy and Illumina or Ion Torrent technology. To ensure FAIR data analysis, this Nextflow pipeline follows nf-core guidelines and use Singularity containers. Pipeline is implemented and available at https://gitlab.com/vtilloy/aspicov.

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Publisher's official version 5 642 KB Open access
S1 Table. Description of samples used in the study. 23 KB Open access
S2 Table. SARS-Cov2 variants of concern (VOC) and interest (VOI). 27 KB Open access
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