Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

[cudamapper] compared to minimap2 #665

Open
wzboy1984 opened this issue Sep 23, 2021 · 0 comments
Open

[cudamapper] compared to minimap2 #665

wzboy1984 opened this issue Sep 23, 2021 · 0 comments

Comments

@wzboy1984
Copy link

Hi,

I've tried doing alignment by cudamapper over 3 datasets, and compared to that by minimap2.
The time costs don't reduce much when compared to minimap2. In some cases, the running speeds of cudamapper are slower than minimap2, as shown in the below table.

  Name wall time(s) mem peak(G) note
data 1 cudamapper 650.63 10.87 v100, 16G
  minimap2_v2.20 1687.86 31.53 -t 32 -k 17 -w 17 -x ava-ont
data 2 cudamapper 11193 39.76 v100, 16G
  minimap2_v2.20 4491 19.21 -t 32 -k 17 -w 17 -x ava-ont
data 3 cudamapper 5958 27.4 NVIDIA TITAN xp, 12G
  minimap2_v2.20 4590 54.02 -t 32 -x ava-ont

Also, the sensitivity of the cudamapper alignments is lower than that of minimap2, which leads to the poorer assembly results based on cudamapper alignments of the 3 above datasets. The algorithm of cudamapper might need to be modified to get alignment results similar to minimap2.

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

1 participant