Assembly graph in GFA format

[sjackman]

Does wtdbg2 support outputting the assembly graph in GFA1 or GFA2 format?

[lh3]

Wtdbg2 outputs intermediate graphs in dot. No final graph like canu/falcon/miniasm, though.

[sjackman]

Consider it a feature request then?

[ruanjue]

There is a script https://github.com/ruanjue/wtdbg2/blob/master/scripts/wtdbg-dot2gfa.pl, it can translate dot files into GFA format.

[sjackman]

Excellent! Could wtdbg2 output a final assembly graph in GraphViz format?

[ruanjue]

Yes, the final assembly graph can be found in prefix.ctg.dot.

[sjackman]

Excellent! Thanks, Jue!

[claczny]

There is a script https://github.com/ruanjue/wtdbg2/blob/master/scripts/wtdbg-dot2gfa.pl, it can translate dot files into GFA format.

Please note that this script expects the prefix.[123].dot files as input.

I tried it with the prefix.ctg.dot to no avail, hence, dot -Tps prefix.ctg.dot -o prefix.ctg.ps should do the trick.

[sjackman]

Ah, so it's not currently possible to convert the final assembly to GFA format?

[ruanjue]

300f189
GFA for prefix.frg/ctg.dot.

[sjackman]

Great! Thanks!

[claczny]

Thanks a lot!