Mapping reads for gap closure in de novo assembly

Question

[criskzimpel]

Hi, I am working with genome sequencing of Mycobacterium bovis. I did the assembly step with ABySS and CLC Genomics Workbench, but it results in few gaps. I was wondering if it is possible to map the reads with the reference genome (available in GenBank) for gap closure.

[mark.ziemann]

Your best bet would be to add some long sequence reads from MiniION or PacBio systems to improve contiguity. If you have Illumina data you could try an error correction tool like BFC to reduce noise. You could try the read mapping approach but it might not work if the unassembled regions are hypervariable or highly repetitive (it would still be an informative result though).