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I'm trying to assemble a nematode genome that we estimate to be 400Mb in length. I have 60x worth of PacBio Sequel data and I've been using HGAP4 (FALCON + Arrow). So far I'm not having much luck getting a good assembly and I'm trying to decide if its worth tweaking parameters more than I already have, or if it would be worth generating more PB coverage.
My primary metric for how good the assembly is has been BUSCO to look at core gene coverage and then simple contig metrics (N50, total length, # contigs, etc...) So far my best assembly has been missing 35 BUSCO core eukaryotic genes, and a fair number of the genes that were found were found > 1 time. Also the total length of contigs we're getting is > 100Mb larger than we expected (although its within the world of possibility that our genome size estimate is wrong). So I suspect this worm's genome may be highly polymorphic. We do have an old assembly but its in pretty bad shape itself (and the reason we want to build a new, better one).
Can anyone suggest arguments for HGAP4 that might help improve contiguity in a genome that is very polymorphic? So far I've tried HGAP4's default params, default params + the 'aggressive' switch, and a range of values for cutoff_length_pr. If I set cutoff_length_pr to just a bit < the mean pre-assembly read length my contiguity goes up and the genome size drops to closer to what I had expected, but I end up losing a few core genes. So I think its really just dropping data that is needed.
Any advice would be appreciated.
My primary metric for how good the assembly is has been BUSCO to look at core gene coverage and then simple contig metrics (N50, total length, # contigs, etc...) So far my best assembly has been missing 35 BUSCO core eukaryotic genes, and a fair number of the genes that were found were found > 1 time. Also the total length of contigs we're getting is > 100Mb larger than we expected (although its within the world of possibility that our genome size estimate is wrong). So I suspect this worm's genome may be highly polymorphic. We do have an old assembly but its in pretty bad shape itself (and the reason we want to build a new, better one).
Can anyone suggest arguments for HGAP4 that might help improve contiguity in a genome that is very polymorphic? So far I've tried HGAP4's default params, default params + the 'aggressive' switch, and a range of values for cutoff_length_pr. If I set cutoff_length_pr to just a bit < the mean pre-assembly read length my contiguity goes up and the genome size drops to closer to what I had expected, but I end up losing a few core genes. So I think its really just dropping data that is needed.
Any advice would be appreciated.