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Old 03-29-2011, 02:59 PM   #1
Location: Davis, CA

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Default Hybrid assembly of PacBio and Illumina

I would like to know how people are handling hybrid assemblies of PacBio and Illumina. Are Velvet or the CLC-Bio good choices?

Thanks for your input
allo is offline   Reply With Quote
Old 03-30-2011, 08:15 AM   #2
Peter (Biopython etc)
Location: Dundee, Scotland, UK

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I know Bastien has been working on PacBio support in MIRA, which already supports Roche 454, Solexa/Illumina and Sanger reads for hybrid assemblies.
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Old 04-26-2012, 12:34 PM   #3
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Location: Birmingham, UK

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ALLPATHS-LG has support for Illumina / Pacbio combined assemblies, but I understand it has quite strict requirements as to the particular type of input you give it. Nevertheless, check it out.
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Old 05-01-2012, 06:27 AM   #4
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There is a plug-in of the latest Celera assembler, PacBioToCA, written by Sergey Koren at NBACC, that uses illumina reads to error-correct PacBio reads and outputs a frg file for OLC assembly in the CA. We have used this to great success for bacterial genomes (with assistance from Sergey and Adam Phillippy). I think that Bastien's approach has been more one-step, i.e. incorporating the reads directly into the assembly, but I haven't attempted to compare the results. The v1.3 software from PacBio purports to support hybrid assembly as well, with claim to be better than the CA approach, but I haven't tried very hard to make it work or compare it rigorously since we already had the other pipeline working before v1.3 was released.
tplsmith is offline   Reply With Quote

hybrid assembly, illumina, pacbio

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