Hello everybody,
My question is regarding strange phenomenon I observed in a recently assembled microbial genome. My genome was sequenced using PacBio library, which generated two contigs, one for the genome and the other for the plasmid.
Then I used previously sequenced Illumina library for verification and error correction of the PacBio assembly, and the results revealed a 60 kbp region with almost doubled coverage (see attached).
I tried to look for SNPs, to check whether these are two regions that were collapsed during the assembly, but there are none of them.
I also checked the pairing of the reads, and I found reads that are overlapping on both edges of the region from normal to high coverage. There are no paired reads on the edges that their pair was mapped to any other region of the genome.
Does any one experienced such coverage issue and knows what is it or how to deal with it?
Thank you,
Eddie
My question is regarding strange phenomenon I observed in a recently assembled microbial genome. My genome was sequenced using PacBio library, which generated two contigs, one for the genome and the other for the plasmid.
Then I used previously sequenced Illumina library for verification and error correction of the PacBio assembly, and the results revealed a 60 kbp region with almost doubled coverage (see attached).
I tried to look for SNPs, to check whether these are two regions that were collapsed during the assembly, but there are none of them.
I also checked the pairing of the reads, and I found reads that are overlapping on both edges of the region from normal to high coverage. There are no paired reads on the edges that their pair was mapped to any other region of the genome.
Does any one experienced such coverage issue and knows what is it or how to deal with it?
Thank you,
Eddie
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