I have been trying to use QUAST to produce icarus output with the coverage across the reference assembly. I am trying to do this with PacBio data and I am having issues getting it to work. I aligned my pacbio reads to the reference using pbalign and input the resulting bam file into the quast command with the --bam option.

It does produce a icarus image but without the coverage info. I think it may not be working as it is not paired data but I am not certain. Has anybody else had the same issue? Does anyone know a fix/how to do it correctly?

Thanks for reading

Matthew gemmell