Tools to generate coverage plots for the sequenced virus reads

Question

[bioinforesearchquestions]

Hi Folks,

I have sequenced virus reads (151 bases, paired-end) samples using MiSeq. I would like to generate coverage plots. Do you recommend any tools to generate it and visualize them?

[GenoMax]

Use Qualimap with your aligned/sorted BAM files.

Answer 1

[Brian Bushnell]

IGV is great for that purpose. It requires a mapped, sorted, indexed bam file as input as well as the reference fasta.