BU-ISCIII/SARS_Cov2_consensus-nf is a bioinformatics analysis pipeline used to analyze SARS-Cov2 Illumina data. The approach followed by this pipeline is to create a consensus genome through mapping, variant calling and consensus genome generation.
The workflow processes raw data from FastQ inputs (FastQC, Trimmomatic), maps the reads (Bowtie2 and Samtools) against the host and the viral reference genome. Optionally, if the data has been obtaine through amplicon sequencing you can use iVar to trim the primers. Then the pipeline calls for variants and annotates them (VarScan, SnpEff), generates a genome sequence consensus (Bgzip and BCFtools) with the variants. Finally we generate a stats report with MultiQC See the output documentation for more details of the results.
The pipeline is built using Nextflow, a bioinformatics workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It comes with docker / singularity containers making installation trivial and results highly reproducible.
The BU-ISCIII/SARS_Cov2 pipeline comes with documentation about the pipeline, found in the docs/ directory:
CREDIT: We inspired in nf-core templates