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bcgsc / tigmint

⛓ Correct misassemblies using linked AND long reads
https://bcgsc.github.io/tigmint/
GNU General Public License v3.0
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Runtime on finding breakpoints #14

Closed JordideRaad closed 6 years ago

JordideRaad commented 6 years ago

Dear Shaun Jackman,

We have recently received our 10x genomics data and currently optimizing our de novo assembly using different tools (bird genome of 1.2GB). To check for assembly errors, I decided to run Tigmint. The mapping step proved to be no problem, however the "finding breakpoints" step in which tigmunt-cut is used, is now running for more than two weeks without anything happening.

Is it expected that this step takes so much time?

Kind regards,

Jordi

lcoombe commented 6 years ago

Hi Jordi,

No, the tigmint-cut step is not expected to take that long. Try using our most recent release (1.1.1) -- 1.1.0 has a significant bug which can cause the tigmint-cut step to take much longer and not cut properly.
For reference, when running tests using a human assembly and setting t=16, this step usually completes in less than 10 minutes.

Hope that helps! Lauren

JordideRaad commented 6 years ago

Dear Lauren,

Thank you very much for the notification. I ran the analyses again today with the new verstion. Indeed, in the newest version tigmint-cut seems to work now.

Kind regards,

Jordi

lcoombe commented 6 years ago

Hi Jordi,

That's great - I'm glad Tigmint is running properly for you now!

Lauren