how to use wtdbg-dot2gfa.pl

ruanjue / wtdbg2

Redbean: A fuzzy Bruijn graph approach to long noisy reads assembly

GNU General Public License v3.0

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how to use wtdbg-dot2gfa.pl #167

Closed csuzhang closed 4 years ago

csuzhang commented 4 years ago

Hi How to use wtdbg-dot2gfa.pl, and any recommend parameter for wtdbg-dot2gfa.pl

Thanks

ruanjue commented 4 years ago

No parameter, run it as gzip -dc dbg.3.dot.gz | wtdbg-dot2gfa.pl >dbg.3.gfa.

ptranvan commented 4 years ago

hi @ruanjue,

I also need the GFA for hi-c scaffolding. What the difference and which one should I use between:

wtdgb2.3.dot.gz  
wtdgb2.ctg.dot.gz
wtdgb2.frg.dot.gz

ruanjue commented 4 years ago

I guess you are needing the .ctg.dot. .frg.dot is for unitigs, the unitigs are more accurate than contigs. .ctg.dot is the final graph comes from unitigs.