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biomedicalinformaticsgroup / Sargasso

Sargasso disambiguates mixed-species high-throughput sequencing data.
http://biomedicalinformaticsgroup.github.io/Sargasso/
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test RNA-seq speed in bisulfite-seq branch #101

Open hxin opened 5 years ago

hxin commented 5 years ago
Data.Name Sargasso.Strategy difference bisulfite master
rna_mouse_10 best 00:00:11 bisulfite_seq=00:13:30 master=00:13:41
rna_mouse_10 conservative -0.0002315 bisulfite_seq=00:12:03 master=00:11:43
rna_mouse_10 permissive -0.0002894 bisulfite_seq=00:14:05 master=00:13:40
rna_mouse_10 recall -0.0002778 bisulfite_seq=00:14:00 master=00:13:36
rna_human_2 best -0.0002083 bisulfite_seq=00:15:33 master=00:15:15

image

hxin commented 5 years ago

No difference in time, as expected. @lweasel

hxin commented 5 years ago

Well, a 10+ seconds delay may be caused by refactoring the namedtuple threshold data into a class, so an extra object is created when checking the threshold.