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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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Is 10x-linked reads availble for TGS-GapCloser? #45

Closed ClarenceHsiang closed 2 years ago

ClarenceHsiang commented 2 years ago

Dear TGS-GapCloser developers:

Good evening.

I would like to use 10x-linked reads for GapClosing, is there any setting that should be modified?

Thank you very much.

adonis316 commented 2 years ago

Thank you for choosing TGS-GapCloser. However, this software tool is designed for third-generation long reads (Oxford nanopore, PacBio) to close gaps. As long fragments are sequenced highly sparsely (~20% coverage) for 10X-linked reads, they cannot provide ATCG sequences to fill gaps.

I would suggest to use NGS short-read gap closer, such as SOAPdenovo GapCloser v1.12 (https://sourceforge.net/projects/soapdenovo2/files/GapCloser/bin/r6/GapCloser-bin-v1.12-r6.tgz/download).

Thanks, Mengyang