15 billions reads ... how long ?

Question

[sebastien.letort]

Hi,

I ran discoSNP on a set of 100 exomes. It runs well.
kissreads2 is running, my log shows that after indexation, there are around 15 billions reads to map. It is looping over read set ("Mapping read set 104" for now), how can I know the total number of read sets ?

Answer 1

[pierre.peterlongo]

Hi,

Thanks for your message Sebastien.

The number of read sets is the one you used as input (in your file of file provided with the -r option).

Currently, the kissread2 phase is the longuest one. We are looking for some ways of making this faster.

Pierre