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ababaian / LIONS

LIONS is a bioinformatic analysis pipeline which brings together a few pieces of software and some home-brewed scripts to annotate a paired-end RNAseq library to detect TE-intiated transcripts
GNU General Public License v3.0
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memory usage and speed up consultant, thanks! #19

Open whiteorchid opened 3 years ago

whiteorchid commented 3 years ago

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!

rpg18 commented 3 years ago

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!

ababaian commented 3 years ago

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.