-S option for pyabpoa

[christopher-vollmers]

Hi,

My lab's Mandalorion and C3POa tools use pyabpoa and it works great. Just every once in a while, we encounter an overlong sequence and pyabpoa stalls for a very long time.

I've noticed that abpoa has the -S option to do seeded alignment, potentially using a lot less memory in the process.
Is that option available for pyabpoa as well? I can't seem to find that info.

Thank you,
Chris

[yangao07]

Hi Chris,

You are right, the python version of abPOA does not have the seeding option right now.
It is possible to add this feature.

I will get back to you later.

Yan

[yangao07]

Also, you may want to try the abPOA program with -S enabled on your data first, to see if you can get the expected result.