Have a genome assembly, what should I do with 15x Pacbio reads?

[lemur2]

Hi everybody,
I am working to improve the assembly of a 400 Mb or so eukaryotic genome. We've done a fair amount of Illumina sequencing already, something like 60X coverage, and we've assembled the genome to an N50 of around 100,000 nt.

So, now we've got another 15X coverage of Pacbio reads, and I'm wondering what to do with them. Should we use them to pull the already assembled contigs together? If so, what software should we use?

Or, should we start from zero and do another de novo assembly, this time a hybrid assembly using both Illumina and Pacbio reads?

If it matters at all, we had a fair amount of bacterial contamination in the DNA sample, but I think we've managed to get rid of most of it using depth of coverage (the bacterial reads were of much higher coverage so were fairly easy to spot).

Any advice welcome. Thanks!

[jbingham]

At this time, there are really only two good options given the genome size and combination of data: pacBioToCA with Celera Assembler, or pb-jelly to fill gaps and join contigs.

The pacBioToCA approach first aligns the Illumina reads against the longest PacBio reads, then makes a consensus. After that, it assembles the raw Illumina data plus consensus PacBio data together.

pb-jelly uses your existing Illumina assembly and fills in the gaps with PacBio.

[lemur2]

Thanks jbingham - I think pb-jelly seems most appealing at the moment, I'll give that a try. Cheers!