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Old 04-10-2018, 11:49 AM   #1
Antony03
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Location: Canada, Quebec

Join Date: Apr 2012
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Default Assembly of a mycete genome with HGAP4

Hello,

I need to assemble a fungus genome for which no information is known. When doing the assembly with canu, I get an assembly of 4918 contigs with a total of 57 123 496 bp. However, with HGAP4, I get an assembly of 2617 contigs with a total of 27,258,314 bp. Why such a big difference? Is it because the genome is diploid and HGAP4 assembles only one haplotype while canu assembles both?

Thank you,

Antony

Last edited by Antony03; 04-10-2018 at 01:02 PM.
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Old 04-11-2018, 08:35 AM   #2
rhall
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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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