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Old 09-10-2018, 11:53 PM   #1
ealamoudi
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Default Polyploid Assemblers

Sorry, I'm new in the field and this may seem like a silly question but I need your help.

How do polyploid genomes (triploid, tetraploid, .... ) are assembled? Which assembler is best to use? Does each subgenome is assembled alone? If yes, then can we use haploid assemblers instead, and then collapse them together?

I asked this because I saw a number of diploid assemblers (such as FALCON) but none for triploid or other polyploids genome.

Thanks in advance.
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Old 09-13-2018, 04:44 AM   #2
colindaven
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Diploid assemblers are very new, and are only being applied by pioneering groups in the last couple of years. To my knowledge most groups are still doing haploid assemblies, and noone has delved into polyploid assemblies with success to date. I don't know how huge projects like the Intl Wheat genome seq consortium deal with these issues. Probably with BAC assemblies, PacBio, Nanopore and other commercial methods.
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Old 09-15-2018, 10:35 PM   #3
ealamoudi
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Yes, diploid assemblers are new in the area, and view of them exists.
So, from what you said I could infer that the complexity of developing polyploid assembler is the reason that there is none in the domain yet. Am I right?

Thanks for the reply.
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