For the purposes of an Illumina only or Illumina+PB assembly, is wgs still being supported or canu or some other successor the recommendation? I understand canu can correct pacbio reads, but I don't think it takes in Illumina reads.
Canu does not support any assembly using Illumina reads. It is designed for only single-molecule sequencing like PacBio or Nanopore. You are welcome to use WGS for PB+Illumina assembly but that mode hasn’t been updated since 2012 and we’re not supporting it because it is significantly slower than PacBio-only assembly and usually results in lower-quality assembly (provided you have sufficient PacBio coverage). If have 20+X of PacBio coverage, you can try Canu in low-coverage mode to get an assembly.
Status: open
Group: v1.0_(example)
Created: Wed Mar 23, 2016 08:04 PM UTC by yasir s
Last Updated: Wed Mar 23, 2016 08:04 PM UTC
Owner: nobody
For the purposes of an Illumina only or Illumina+PB assembly, is wgs still being supported or canu or some other successor the recommendation? I understand canu can correct pacbio reads, but I don't think it takes in Illumina reads.
Canu does not support any assembly using Illumina reads. It is designed for only single-molecule sequencing like PacBio or Nanopore. You are welcome to use WGS for PB+Illumina assembly but that mode hasn’t been updated since 2012 and we’re not supporting it because it is significantly slower than PacBio-only assembly and usually results in lower-quality assembly (provided you have sufficient PacBio coverage). If have 20+X of PacBio coverage, you can try Canu in low-coverage mode to get an assembly.
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Support Requests: #27