TY - JOUR
T1 - VODKA2
T2 - a fast and accurate method to detect nonstandard viral genomes from large RNA-seq data sets
AU - Achouri, Emna
AU - Felt, Sébastien A.
AU - Hackbart, Matthew
AU - Rivera-Espinal, Nicole S.
AU - López, Carolina B.
N1 - Publisher Copyright:
© 2024 Achouri et al. This article, published in RNA, is available under a Creative Commons License (Attribution-NonCommercial 4.0 International), as described at http://creativecommons.org/licenses/by-nc/4.0/.
PY - 2024/1
Y1 - 2024/1
N2 - During viral replication, viruses carrying an RNA genome produce non-standard viral genomes (nsVGs), including copy-back viral genomes (cbVGs) and deletion viral genomes (delVGs), that play a crucial role in regulating viral replication and pathogenesis. Because of their critical roles in determining the outcome of RNA virus infections, the study of nsVGs has flourished in recent years, exposing a need for bioinformatic tools that can accurately identify them within next-generation sequencing data obtained from infected samples. Here, we present our data analysis pipeline, Viral Opensource DVG Key Algorithm 2 (VODKA2), that is optimized to run on a parallel computing environment for fast and accurate detection of nsVGs from large data sets.
AB - During viral replication, viruses carrying an RNA genome produce non-standard viral genomes (nsVGs), including copy-back viral genomes (cbVGs) and deletion viral genomes (delVGs), that play a crucial role in regulating viral replication and pathogenesis. Because of their critical roles in determining the outcome of RNA virus infections, the study of nsVGs has flourished in recent years, exposing a need for bioinformatic tools that can accurately identify them within next-generation sequencing data obtained from infected samples. Here, we present our data analysis pipeline, Viral Opensource DVG Key Algorithm 2 (VODKA2), that is optimized to run on a parallel computing environment for fast and accurate detection of nsVGs from large data sets.
KW - RNA-seq
KW - VODKA2
KW - bioinformatics
KW - defective viral genomes
KW - viral genomes
UR - http://www.scopus.com/inward/record.url?scp=85179926938&partnerID=8YFLogxK
U2 - 10.1261/rna.079747.123
DO - 10.1261/rna.079747.123
M3 - Article
C2 - 37891004
AN - SCOPUS:85179926938
SN - 1355-8382
VL - 30
SP - 16
EP - 25
JO - RNA
JF - RNA
IS - 1
ER -