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iqbal-lab / cortex

reference free variant assembly
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Add GFA support #3

Closed iqbal-lab closed 8 years ago

iqbal-lab commented 9 years ago

See https://github.com/pmelsted/GFA-spec

noporpoise commented 9 years ago

GFA output is already in McCortex, so the following will work with Cortex graphs:

mccortex31 unitigs --gfa graph.ctx > graph.gfa
iqbal-lab commented 9 years ago

That's a great workaround for now, thanks!

noporpoise commented 9 years ago

BTW You can create a GFA file from a sequence file without writing the Cortex graph file to disk:

mccortex31 build -k 31 -s Example --seq in.fa - | mccortex31 unitigs --gfa - > graph.gfa
iqbal-lab commented 9 years ago

Hurrah for Mccortex! Thanks Isaac.

On 1 September 2015 at 11:13, Isaac Turner notifications@github.com wrote:

BTW You can create a GFA file from a sequence file without writing the Cortex graph file to disk:

mccortex31 build -k 31 -s Example --seq in.fa - | mccortex31 unitigs --gfa - > graph.gfa

— Reply to this email directly or view it on GitHub https://github.com/iqbal-lab/cortex/issues/3#issuecomment-136663166.

iqbal-lab commented 8 years ago

Confirmed.