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Maggi-Chen / Inspector

A tool for evaluating long-read de novo assembly results
MIT License
29 stars 9 forks source link

Using nanopore ultra-long reads to correct structural error #14

Closed tinyfallen closed 4 months ago

tinyfallen commented 2 years ago

Hi dear developer,

I tried to use nanopore ultra-long reads to correct structural error in my hifi assembly. The inspector.py module did detect 443 structural error in the structural_error.bed, however the inspector-cor directly said

Inspector Assembly Fail chr012182326218242397exp ...

as flye seemed not working. I wonder if it caused by the length of the reads were usually longer than 50kb and sometimes 100kb.

I have tested to assemble a read_ass_chr01100958203100958204153col.fa by flye with default parameter which get a 23kb contig while the longest reads in the fasta file was 108640bp. And the program took nearly an hour to run for 15 reads in the fasta with a mean length of 90461 bp.

Could you please give me some suggestions to correct the structural error in my hifi assembly? Thanks a lot!

tinyfallen commented 4 months ago

已收到您发送的邮件！

unavailable-2374 commented 1 week ago

Hey! I’ve been encountering a similar issue recently. I’m using HiFi reads to correct an assembly, but the inspector tool reports a number of errors, such as:

Inspector Assembly Fail XXXX

Were you able to resolve this problem? If so, I’d greatly appreciate any advice or suggestions you might have.

Thanks a lot!

tinyfallen commented 1 week ago

已收到您发送的邮件！