SARS-CoV-2 variant prediction using Read It And Keep, fastp, bbmap and iVar

COVID-19: variation analysis on ARTIC ONT data

This workflow for ONT-sequenced ARTIC data is modeled after the alignment/variant-calling steps of the ARTIC pipeline. It performs, essentially, the same steps as that pipeline’s minion command, i.e. read mapping with minimap2 and variant calling with medaka. Like the Illumina ARTIC workflow it uses ivar for primer trimming. Since ONT-sequenced reads have a much ...

COVID-19 sequence analysis on Illumina Amplicon PE data

This workflow implements an iVar based analysis similar to the one in ncov2019-artic-nf, covid-19-signal and the Thiagen Titan workflow. These workflows (written in Nextflow, Snakemake and WDL) are widely in use in COG UK, ...

COVID-19: variation analysis on ARTIC PE data

The workflow for Illumina-sequenced ampliconic data builds on the RNASeq workflow for paired-end data using the same steps for mapping and variant calling, but adds extra logic for trimming amplicon primer sequences off reads with the ivar package. In addition, this workflow uses ivar also to identify amplicons affected by primer-binding site mutations and, if possible, excludes reads derived from such ...