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BGI-Qingdao / TGS-GapCloser

A gap-closing software tool that uses long reads to enhance genome assembly.
GNU General Public License v3.0
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How to check the correctness of filling gaps? #75

Closed luca-Wang closed 7 months ago

luca-Wang commented 11 months ago

Hello, my genome has 10G and contains 500 gaps. After running the tgs-gapcloser software, I successfully filled 90 gaps. May I ask how to check the correctness of filling these gaps one by one? I used IGV software to check， whether there is a quick way to identify reads that support each gap and verify their correctness？

Thanks in advance!

adonis316 commented 9 months ago

If you have a reference genome for this species or closely related species, then you can align and compare these closed gaps with the reference using minimap2.

If this is a de novo project without any reference genome, then checking the alignments of reads to the gap region is a fast but efficient measure to check the correctness. You can directly analyze the alignment file in SAM/PAF format. Plus, IGV is a good option to visualize these alignments.

Thanks, Mengyang