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DecodeGenetics / Ratatosk

Hybrid error correction of long reads using colored de Bruijn graphs
BSD 2-Clause "Simplified" License
96 stars 7 forks source link

Feature request: Reference guided correction - locally #14

Closed rahulvrane closed 4 years ago

rahulvrane commented 4 years ago

Hi I was wondering if we are able to run ref guided correction locally. I do have access to required CPU #'s and RAM on 1 single machine..

Thanks a ton Cheers

philres commented 4 years ago

I second that. Would be great to have that!

philres commented 4 years ago

Also, would be happy to do some testing if that'd help.

GuillaumeHolley commented 4 years ago

Sure, I will try to make something with GNU Parallel :) I'll keep the issue open until this is online.

philres commented 4 years ago

Nice, thanks!

On Mon, 21 Sep 2020, 13:35 Guillaume Holley, notifications@github.com wrote:

Sure, I will try to make something with GNU Parallel :) I'll keep the issue open until this is online.

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/DecodeGenetics/Ratatosk/issues/14#issuecomment-696085317, or unsubscribe https://github.com/notifications/unsubscribe-auth/AARXMHC3ZIB2J3UYPJUA77TSG5CBRANCNFSM4RT6ABCA .

GuillaumeHolley commented 4 years ago

Hi @rahulvrane and @philres ,

I just pushed a script to run Ratatosk with the reference-guiding on a single-machine (turns out that GNU Parallel wasn't needed after all). README was updated. It works but hasn't been tested thoroughly so I would appreciate any feedbacks and suggestions.

Guillaume

GuillaumeHolley commented 4 years ago

Also, I'll be pushing the v0.3 of Ratatosk next week. It comes with a new key feature for the reference-guiding that I'll keep as a surprise for now :)

philres commented 4 years ago

Awesome, thanks will give it a go!

Philipp

On Thu, 1 Oct 2020, 12:02 Guillaume Holley, notifications@github.com wrote:

Also, I'll be pushing the v0.3 of Ratatosk next week. It comes with a new key feature for the reference-guiding that I'll keep as a surprise for now :)

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/DecodeGenetics/Ratatosk/issues/14#issuecomment-702058375, or unsubscribe https://github.com/notifications/unsubscribe-auth/AARXMHGPH7YS2MBY2VUQCCDSIROTZANCNFSM4RT6ABCA .

rahulvrane commented 4 years ago

Epic - thanks for that! I'll give this a swirl and keenly await 0.3! Cheers Rahul