How many reads do I need for hybrid assembly

Question

I have Illumina and PacBio reads and I would like to use dbg2olc for hybrid assembly.

Part of dbg2olc is SelectLongestReads which select reads that sum to total_length of bases.

How many bases do I need for a 1.8G allotetraploid to remain?

Answer 1

I have never used dbg2olc. However other OLC assemblers managed to do a solid assembly from 20x of corrected long reads. But obviously, the more the better.

In you case of allotetraploid, you need to figure out if the heterozygosity is sufficient to separate haplotypes of not and adjust parameters of the assembler. For instance in bdelloid rotifers the tetraploid genome has an AA'BB' structure, all the assemblies were able to separate A and B, but not A and A' and B and B'. I guess an allotetraploid could have a similar structure.

It would be good to know what you are dealing with and what is your goal in the assembly. Do you want a single haplotype?

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You can check the genome structure using short reads by smudgeplot, a tool I made (yes, it's a shameless plug).