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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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Use of HiFi reads of the PacBio Sequel Systems ? #24

Closed agroppi closed 3 years ago

agroppi commented 3 years ago

Is it possible to use HiFi reads produced using the circular consensus sequencing (CCS) mode on one of the PacBio Sequel Systems ? If yes, what would be the usage arguments for TGS-GapCloser ? Thanks

adonis316 commented 3 years ago

Hi, The base-calling accuracy of HIFI CCS reads is usually >99%. You might use them to directly close gaps without any error corrections by "--tgstype pb --ne". However, if you have sufficient NGS or CCS reads, you can still improve the read accuracy by polishing the gap-closing regions. Then the parameters would be the same as PacBio CLR reads "--tgstype pb" + error correction.

Thanks, Mengyang Xu

agroppi commented 3 years ago

Thanks for you answer. I'll give it a try Cheers from Bordeaux (France)

EvoMedLab commented 3 years ago

I have a modification of this issue. I have a rather contiguous 3gb assembly made from only CCS reads, so accuracy is excellent, but there are still gaps to close.

I have recently acquired considerable (>100x) Oxford Nanpore reads that have excellent read length, but of course poor accuracy. I do not want to alter the HiFi sequence at all, but would like to link the contigs with the ON reads. Is there a way to ensure the current contigs are not modified at all, but are still able to be pseudo-scaffolded with TGS-GC?

adonis316 commented 3 years ago

Hi, TGS-GapCloser will not modify the input contigs while closing gaps with additional long reads. You can use a few of ultra-long Nanopore reads (~10x, considering computational consumption) to close gaps in CCS-based assemblies.

However, the latest version of TGS-GapCloser does not support further scaffolding. You might try other software tools, such as SSPACE-LongRead, SLR…

Hanjiangna commented 6 months ago

what then meaning of "the latest version of TGS-GapCloser does not support further scaffolding" ?