Combined assembly analysis (short reads + long reads)

[XCL]

Dear NGS Experts,

I have a question about combined genome assembly.

We have 75X Hiseq sequencing of an animal species genome (about 3Gb genome size) together with 50X Pacbio Sequel system, now, we would like to make a combined assembly analysis of these 350Gb data. Anybody knows any tools for this kind of analysis?

Many thanks.

[GenoMax]

For reference, cross-posted: https://www.biostars.org/p/187524/

[XCL]

For reference, cross-posted: https://www.biostars.org/p/187524/

Hi GenoMax, thanks a lot. Exactly, if there is any tool which can use the short reads to correct the error on the long reads, that would be great. Such tools should be very useful for combined assembly analysis.

[GenoMax]

Did you see this link: https://github.com/PacificBioscience...Bio-Long-Reads pacBioToCA is the tool you want.

[XCL]

Did you see this link: https://github.com/PacificBioscience...Bio-Long-Reads pacBioToCA is the tool you want.

Dear GenoMax, thank you very much, that link is quite useful. There is another problem/situation that the genome is with very high heterozygosity, whether the five hybrid assemblers (pacBioToCA, ECTools, SPAdes, Cerulean, dbg2olc) can deal with such situation?

[GenoMax]

You are not going to know until you try. Sounds to me like someone is going to stay busy for a while. Hope you have access to some beefy compute resources since this is going to take a lot of RAM etc.

[wdecoster]

The term you're looking for is "hybrid assembly".

[XCL]

You are not going to know until you try. Sounds to me like someone is going to stay busy for a while. Hope you have access to some beefy compute resources since this is going to take a lot of RAM etc.

Right, we will try them all. The enough RAM is always important until the transfer rate of sad can reach at least 5GB/s. Thank you again.

[GenoMax]

I would suggest engaging with PacBio tech support early for this challenging project. Dr. Hall (rhall) from PacBio participates on this forum and he may be a good resource for hints.

If you are getting PacBio data from a sequence provider then be sure to ask for raw data files (*.h5). These would be needed for some of the tools we have discussed.

[fanli]

There was a thread floating around here somewhere suggesting that you use PacBio reads for assembly and Illumina reads to do error correction, etc. afterwards.