nanopore data

[PWSmit]

Hi, quick question, would this also work on nanopore data (10.4 flow cells)? what would be the optimal settings to run ska2 on?

thanks! Pieter

[johnlees]

I'm guessing that if you assemble the data first and use the fastas with ska build you might get decent results, but using the reads directly almostly certainly won't work because our filtering model is for short read data.

But we haven't tested, so if you try please do let us know whether it works or not as that will also help us potentially target this use in future!

[rderelle]

If the Nanopore reads correspond to the last chemistry version (>99% accuracy), SKA2 might work from raw reads. One option would be to lower the min-count threshold when using the ska build function (e.g. from 5 to 3).

Then you could check if the results make sense using the ska nk function: the number of split k-mers in each sample should be similar to the bug genome size (if known). But this is very much experimental.

[johnlees]

Closing as stale