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COMBINE-lab / pufferfish

An efficient index for the colored, compacted, de Bruijn graph
GNU General Public License v3.0
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pufferfish for assembly #3

Closed SilasK closed 4 years ago

SilasK commented 6 years ago

Hello, your project seems very interesting.

Is it already possible to use it for assembly? If yes could you give me a hint where to start?

fataltes commented 6 years ago

Hi @SilasK ,

Thanks for your interest.

I know it is probably so late and I really apologize for not replying sooner.

Pufferfish is basically designed as an index data structure on a set of known references plus the api required to query the set for a short sequencing read. Unfortunately, that means it is likely not useful to you for the purposes of assembly. It's basically an index designed for mapping/aligning short read sequences against a set of references --- and will also eventually be useful for assembly comparison (i.e. comparing references in terms of their De Bruijn graph paths). However, pufferfish does not, itself, perform any assembly.

-- Fatemeh