-
Notifications
You must be signed in to change notification settings - Fork 101
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
Optimise parameters for minimap2 alignments #446
Comments
One likely contender is the minibatch option
So using default mode, I'll do a few tests with this later, but first I'll focus on k-mer size. |
Heng Li suggested >> Due to the reduced alphabet, you could probably increase the k-mer size such that "mid_occ" in stderr is about several hundred. I have done a few tests now with 10K and 100K PacBio EM-seq test reads (5kb), and it seems pretty obvious that we can achieve a decent speed-up by moving away from the default For the time being, I will change the kmer size to |
Using a k-mer length of 20 as a sweet spot, I tested a few different variations of the minibatch size ( For our specific application, the default of Going forward I think we'll settle for for a combination for |
Test on 100,000 reads:
This is a speed-up of ~45-fold, along with a 3-fold reduction in memory. Pretty happy with these results. |
I looked at the possibility of improving the alignment speed via parallelisation within Bismark. The default mode (i.e.
So one should probably reserve 14 cores and 40G RAM for each level of The results show that there is a decent level of additional speed-up to be had if the resources are plentiful, even though there might be diminishing returns at some point. |
Lastly, I looked at the multi-threading capacity within each minimap2 invocation: Using at least For the time being I would like to settle on the following parameters as the default: |
Some of the long read alignments take a very long time indeed, so I am sure there is plenty of scope for improvement.
The text was updated successfully, but these errors were encountered: