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ganlab / GALA

Long-reads Gap-free Chromosome-scale Assembler
MIT License
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How to get misassembly-free draft #9

Closed lyrk50 closed 3 years ago

lyrk50 commented 4 years ago

Hi, I ran the ccm module and got three different new_draft.fa. Then I want to ran bwa index misassembly-free draft, but I have problems about how to get misassembly-free draft. Should I merge three different new_draft.fa? Hope to get your advice.

mawad89 commented 4 years ago

Hi You can get the misassembly-free draft after run from MDM module.

  1. use mdm to detect the mis-assembly.
  2. use newgenome to produce misassembly-free draft from mdm output.

Also, it is possible to use any other method to detect and trim misassembled contigs then you can run the command. We developed each module to be completely independent.

lyrk50 commented 4 years ago

Hi Mohamed, Thanks for your reply. I use newgenome and get new_draft_01.fa new_draft_02.fa new_draft_03.fa. Then I want to run LGAM , should I merge three fasta files to get a new fasta or run them one by one? Hope to get your advice. Lynn

mawad89 commented 4 years ago

Hi Lynn; Run them one-by-one separately. In practice, if you have a lot of Preliminary drafts. using LGAM with 1-3 drafts gives a very good results. If anything unclear just drop a message. All the best Mohamed

lyrk50 commented 4 years ago

Hi Mohamed, Thanks for your reply. I saw a sentence in your paper that This flexible framework also allows us to integrate data from various technologies, such as Hi-C, genetic maps, a reference genome and even motif analyses, to generate gap-free chromosome-scale assemblies. How can I use Hi-C data in this workflow? Best wishes Lynn

mawad89 commented 4 years ago

Hi Lynn You can use the Hi-C as one of preliminary assemblies. For Example you can use SALSA or Juicer, then use their draft as a preliminary draft. GALA enhanced Hi-C draft contiguity, correct its errors or misassemblies, and closed the gaps.

All my best wishes Mohamed

lyrk50 commented 4 years ago

Hi Mohamed, Thanks you for the response. If I use Juicer on my Hi-C data, which file format can be used as a preliminary draft? It seems like that no output file format is fasta. Best wishes Lynn

mawad89 commented 4 years ago

Hi Lynn

Juicer gives a fasta file named as assembly.FINAL.fasta. SALSA gives a fasta file named scaffolds_Final.fasta. GALA takes any of this files

Best wishes Mohamed