Question: Ideal coverage required for PacBio error correction using HGAP
gravatar for Felix Francis
4.6 years ago by
Felix Francis490
United States/University of Delaware
Felix Francis490 wrote:

What is the ideal PacBio coverage required for error correction (consensus polishing) using HGAP (by only using PacBio reads)? How effective is this approach in error correction?

How does this approach compare with hybrid error correction using Illumina short reads (assuming the reads are from a homozygous genome)?

ADD COMMENTlink modified 4.6 years ago • written 4.6 years ago by Felix Francis490
gravatar for Biomonika (Noolean)
4.6 years ago by
State College, PA, USA
Biomonika (Noolean)3.1k wrote:

For HGAP only, recommended coverage would be 60x-100x (more repetitive genome, the higher). It seems to be very effective for small microbial genomes (you could end up with 1 or 2 contigs), it has issues for larger (and eukaryotic) genomes.  

Comparison with hybrid approach will depend on many factors, most importantly genome size and complexity. For small microbial genomes, I wouldn't bother with Illumina and would do just PacBio and HGAP.

ADD COMMENTlink written 4.6 years ago by Biomonika (Noolean)3.1k

Thanks for the information. So far  for microbial genome we dont need any error correction with illumina reads. Do you have any idea after HGAP we can get many repeated contigs . How to deal with that?? You have to remove by visually or any other approach ??


ADD REPLYlink written 4.6 years ago by HG1.1k
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