memory usage and speed up consultant, thanks!

Open whiteorchid opened this issue 5 years ago • 2 comments

Hi dear authors,

May I know how much memeory is proper for the running of lions, is there a way to speed up the run process, it takes more thant 3 days to process the data of 100M paired reads.

Thanks!

Aug 17 '20 20:08 whiteorchid

Hi @whiteorchid ,

Did you manage to speed up the run process? I am interested in running LIONS to process large datasets.

Thank you in advance!

Oct 04 '20 11:10 rpg18

Sorry about the slow response, LIONS has had to take a bit of a back-burner with COVID19.

The pipeline uses Tophat2/Cufflinks for alignment and assembly which is a bit out-dated by this point. If you have already aligned files and assemblies this will greatly speed up the run-time of LIONS as it will only really have to go through the python scripts to find reads that are possibly chimeric. It's still not "fast" by any means, but you can shave off about 80% of the overall compute time with this.

Oct 05 '20 20:10 ababaian