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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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Conda invoke #37

Closed ardy20 closed 3 years ago

ardy20 commented 3 years ago

Hi

I am trying to use your tool but I do not know how to run it through conda. I use the following but I get error command not found:

TGS-GapCloser.sh --thread 24 --scaff MJ_hifiasm_assembly.fa --reads mj.combined.fasta --tgstype pb --output out_hifiasm-gapclose --ne

adonis316 commented 3 years ago

Hi, The command should be "tgsgapcloser". For example, in your case: "tgsgapcloser --thread 24 --scaff MJ_hifiasm_assembly.fa --reads mj.combined.fasta --tgstype pb --output out_hifiasm-gapclose --ne".

Note that only scaffold sequences with unknown bases "N" can be filled.

Thanks, Mengyang

ardy20 commented 3 years ago

Hi Thanks What is the other option to fill gaps? I do not have "N" in my scaffolds but would like to reduce the number of contigs. I have HiFi reads that have high accuracy (99.9%). Therefore, I won't like to use the polish option with Pilon or Racon. More guidance is appreciated. Regards Ardy

adonis316 commented 3 years ago

TGS-Gapcloser requires contig relations provided by scaffolding to connect contigs and reduce the contig number. You might need a scaffolder to build scaffolds first, and then close gaps (replace N's) between contigs within the same scaffold by TGS-Gapcloser.