Construct a graph from several fasta sequences

[José Alejandro Romero Herrera]

Hi!

So, I want to construct a graph using Cortex from several fasta sequences. Then i would like to align and map some reads that I have to the graph and extract the variants and read depth of the graph. Is is possible to do this with your software?

Thanks,


Alex.

[José Alejandro Romero Herrera]

Hi!

So, I want to try something new in my department. I have some reference genomes that are very similar and I would like to construct an unique graph using Cortex. Then I would align and map some reads to this graph and analyze the result. Is it possible to do so with your software?

Thanks,

Alex.

[Zamin Iqbal]

Basically we have an alternate approach to do what Erik Garrison is doing with vg.

It won't be available for several months though, so I'd play with vg for now

Z

[Erik Garrison]

I'm pretty close to having something usable at the scales (10s of MB) that José is working with.

The basic problem is making alignment of the sequences against graphs of that size more efficient. I'm in the process of debugging what I've got.

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