How to use pacbio reads to join contigs

Question

[934963534]

Hello everyone!

I have some pre-assembled contigs and want to join and extend the contigs using pacbio reads. I tried DBG2OLC on the contigs but the result shows that the contigs are even shorter.

Does anybody know reasons or are there any other tools to join contigs with pacbio reads?

Thanks for your answer!

[Rohit]

Do you have enough coverage i.e. 10X for pacbio. Since DBG2OLC requires multiple alignment of the pacbio reads, if there is lower coverage, It might be easier to clarify if you provide the actual command used, since it doesn't help you have a higher kmer_coverage threshold and low sequencing coverage. If you have pacbio corrected data, then PBJelly scaffolds

Answer 1

[h.mon]

There are indeed some tools, PacBio site points to at least two, FGAP and GMcloser:

https://www.pacb.com/publications/fgap-an-automated-gap-closing-tool/

https://www.pacb.com/publications/gmcloser-closing-gaps-in-assemblies-accurately-with-a-likelihood-based-selection-of-contig-or-long-read-alignments/

What is the quality of the assembly? Are your PacBio reads error-corrected? Did you align the pre- and post-correction contigs? Although I don't know DBG2OLC, one possible reason for the "even shorter" contigs is that DBG2OLC could be breaking chimeric contigs, as per PacBio reads indication - but again, I don't even know if DBG2OLC performs such correction.