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Viruses
. 2022 Jan 23;14(2):217.
doi: 10.3390/v14020217.
ViralFlow: A Versatile Automated Workflow for SARS-CoV-2 Genome Assembly, Lineage Assignment, Mutations and Intrahost Variant Detection
Filipe Zimmer Dezordi 1 , Antonio Marinho da Silva Neto 2 , Túlio de Lima Campos 2 , Pedro Miguel Carneiro Jeronimo 3 , Cleber Furtado Aksenen 3 , Suzana Porto Almeida 3 , Gabriel Luz Wallau 1 , On Behalf Of The Fiocruz Covid-Genomic Surveillance Network
Affiliations
- PMID: 35215811
- DOI: 10.3390/v14020217
Abstract
The COVID-19 pandemic is driven by Severe Acute Respiratory Syndrome coronavirus 2 (SARS-CoV-2) that emerged in 2019 and quickly spread worldwide. Genomic surveillance has become the gold standard methodology used to monitor and study this fast-spreading virus and its constantly emerging lineages. The current deluge of SARS-CoV-2 genomic data generated worldwide has put additional pressure on the urgent need for streamlined bioinformatics workflows. Here, we describe a workflow developed by our group to process and analyze large-scale SARS-CoV-2 Illumina amplicon sequencing data. This workflow automates all steps of SARS-CoV-2 reference-based genomic analysis: data processing, genome assembly, PANGO lineage assignment, mutation analysis and the screening of intrahost variants. The pipeline is capable of processing a batch of around 100 samples in less than half an hour on a personal laptop or in less than five minutes on a server with 50 threads. The workflow presented here is available through Docker or Singularity images, allowing for implementation on laptops for small-scale analyses or on high processing capacity servers or clusters. Moreover, the low requirements for memory and CPU cores and the standardized results provided by ViralFlow highlight it as a versatile tool for SARS-CoV-2 genomic analysis.
Keywords: SARS-CoV-2; genomic variants; genomics; genotyping; software; virus bioinformatics; viruses.