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chhylp123 / hifiasm

Hifiasm: a haplotype-resolved assembler for accurate Hifi reads
MIT License
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False inserts over duplicated regions (TRBV12-3/4) #665

Closed FlexLuthORF closed 5 months ago

FlexLuthORF commented 5 months ago

image image image Dotplot of comparison between TRBV12-3 and TRBV12-4: image Link to assembly.bam(~40mb): https://drive.google.com/file/d/1K_g3lHgRwhILkfe_6tGPuHUOytGXNQYT/view?usp=sharing Link to ccs_to_ref.bam(~500mb): https://drive.google.com/file/d/1u0emZv_UtHj1UKhOpD3mVjEasH76bjLn/view?usp=sharing

Hifiasm is occasionally inserting what appears to be a false insert that is not supported by any ccs reads that combines TRBV12-3 and TRBV12-4. Is this expected? Are there any parameters that would help resolve this issue?

How hifiasm was run: pipeline.sh.txt

FlexLuthORF commented 5 months ago

I did just find one read with a supposed large insert over TRBV12-4 that may have some relation. image

FlexLuthORF commented 5 months ago

image It was a real seg-dupe