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bioinfologics / satsuma2

FFT cross-correlation based synteny aligner, (re)designed to make full use of parallel computing
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Satsuma for more than 2 species #9

Closed madzafv closed 5 years ago

madzafv commented 6 years ago

Hi! is it possible to run satsuma for more than 2 species at the same time? Lets say 3. If not would you advise on any other tool? Thanks!

grabherr commented 6 years ago

Hi,

Currently not, that was the plan for Satsuma 3; have you checked the usual suspects, lastz etc.? Do you need to do his truly reference independent?

Cheers,

On 2018-04-05 23:00, Madza Farias-Virgens wrote:

Hi! is it possible to run satsuma for more than 2 species at the same time? Lets say 3. If not would you advise on any other tool? Thanks!

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madzafv commented 6 years ago

Hey! thanks for the quick reply! Yeah I was intending to build a whole-gen tree between the 3 species using SATe and I think I would need to filter for synteny using a common ref. Maybe I'm making things more complicated than they need to be? Obviously new to this...

mictadlo commented 6 years ago

Using usual suspects, like for example lastz, how is it possible to convert it to MizBee format?

jonwright99 commented 5 years ago

I guess you would have to write a custom script to convert the output to MizBee format.