Hello Every body!
Is there anybody here who has used Pacbio for Bacterial Genome sequencing with not more than 10x coverage? what was the result?
I mean, concerning new Pacbio kits capabilities for producing of reads with mean length of more than 10kbp, is it essential to have more coverage in denovo genome assembly? I think by having reads with mean length of 10kbp , a lower coverage (10x) is enough.
Any better idea?
Best wishes!
Hi Sajad,
Unfortunately, for whole genome sequencing using pacbio 10x coverage is not enough for de novo assemblies, you have to have >80x, as pacbio generates relatively high error rate, the HGAP assembler algorithm could not be able to resolve the these errors with coverage less than 80x. However, you still can remove these errors with a hybrid approach using Illumina hiseq pair ends reads mapped them to the pacbio reads, but I'm not pretty sure if 10x pacbio coverage is enough for such approach.
Kind Regards
Studies you see with PacBio sequencing at the 10X level are probably using PB long reads for scaffolding, as you are not going to get a very high quality assembly with that coverage on its own. More likely in supplement to high coverage short read data (say 50-100X) as this is cheaper to generate.
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