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-   -   Assembly of a mycete genome with HGAP4 (http://seqanswers.com/forums/showthread.php?t=81739)

Antony03 04-10-2018 10:49 AM

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

rhall 04-11-2018 07:35 AM

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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