Question

Tools to generate coverage plots for the sequenced virus reads

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6.6 years ago

bioinforesearchquestions ▴ 370

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?

coverage SNP DNAseq Virus • 1.8k views

ADD COMMENT • link updated 6.6 years ago by Brian Bushnell 20k • written 6.6 years ago by bioinforesearchquestions ▴ 370

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Use Qualimap with your aligned/sorted BAM files.

ADD REPLY • link 6.6 years ago by GenoMax 141k

score 2 · Answer 1 · 2017-09-27

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6.6 years ago

Brian Bushnell 20k

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

ADD COMMENT • link 6.6 years ago by Brian Bushnell 20k