sars-cov-2 analysis: signal
Try signal
This is a complete standardized workflow the assembly and subsequent analysis for short-read viral sequencing.
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Briefly, raw reads undergo qc using fastqc (Andrews) before removal of host-related reads [...] After this, reads undergo adapter trimming and further qc [...] Reads are then mapped to the viral reference [...] After this, iVar is used to generate a consensus genome and variants are called [...] Coverage statistics are calculated using bedtools before a final QC [...] Finally, data from all samples are collated via a post-processing script into an interactive summary for exploration of results and quality control.