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Old 04-11-2018, 07:35 AM   #2
rhall
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Location: San Francisco

Join Date: Aug 2012
Posts: 322
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It's possible that ploidy could account for some of the difference, but it is unlikely that it is that simple. Using default parameters I wouldn't expect Canu to not collapse haplotypes and Falcon to fully collapse, although with the correct parameters and enough divergence between haplotypes both assemblers theoretically could.
Some things to try:
1. Align assemblies to one another to see what the difference actually is, for a quick visulization, http://assemblytics.com/
2. Look at the alternate contigs in the HGAP.4 assembly, <HGAP.4 job dir>/tasks/falcon_ns.tasks.task_falcon2_run_asm-0/a_ctg.fa. HGAP.4 is based on Falcon so does generate contigs for possible alternate haplotypes http://pb-falcon.readthedocs.io/en/latest/
Some more resources on diploid assembly: http://pb-falcon.readthedocs.io/en/l...PacBioHops.pdf
http://pb-falcon.readthedocs.io/en/l...idsPAG2018.pdf
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