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mikolmogorov / Flye

De novo assembler for single molecule sequencing reads using repeat graphs
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question: min coverage trimming? #726

Closed kevfengler227 closed 1 week ago

kevfengler227 commented 1 month ago

I am trying to use flye for targeted assembly of ONT reads to manually fill gaps in T2T assemblies by assembling the flanking and soft-clipped reads aligned at a gap. This works pretty well except for the ends of the targeted contig have low-coverage and consequently low accuracy where the coverage drops at the tails (down to 1x at the ends). Is there a way to just output the assembled bases above a certain coverage threshold?

mikolmogorov commented 1 month ago

@kevfengler227 you can find per-based coverage of polished contigs in the 40-polishing/base_coverage.bed.gz file. You should be able to use it for trimming low-quality ends.

kevfengler227 commented 1 month ago

OK, thanks. Yes, I found that file but I was hoping for a parameter that could do the same thing, like minimal base coverage or someway to force the desired behavior. I am selecting reads that align to a given target position, so it's pretty much a vertical stack of reads, but length outliers are making the ends lower quality.

mikolmogorov commented 1 month ago

Currently there is now such parameter.

mikolmogorov commented 1 week ago

Close due to inactivity, feel free to reopen if there are any follow ups!