Software Open Access
Harshil Patel; Sarai Varona; Sara Monzón; Jose Espinosa-Carrasco; Michael L Heuer; Gisela Gabernet; MiguelJulia; Stephen Kelly; Katrin Sameith; Maxime Garcia; jcurado
[1.0.0] - 2020-06-01
Initial release of nf-core/viralrecon, created with the nf-core template.
This pipeline is a re-implementation of the SARS_Cov2_consensus-nf and SARS_Cov2_assembly-nf pipelines initially developed by Sarai Varona and Sara Monzon from BU-ISCIII. Porting both of these pipelines to nf-core was an international collaboration between numerous contributors and developers, led by Harshil Patel from the The Bioinformatics & Biostatistics Group at The Francis Crick Institute, London. We appreciated the need to have a portable, reproducible and scalable pipeline for the analysis of COVID-19 sequencing samples and so the Avengers Assembled!
parallel-fastq-dump; if required)
cat; if required)
iVar; amplicon data only)
picard; removal optional)
iVar variants and consensus||
Cutadapt; amplicon data only)