Kristoffer

Multithreading

16

Hi @rcedgar, I ran URMAP in my benchmark on short-read aligners and noticed that, while it is very fast, it has low CPU usage (between 10% and 90%) regardless of...

terminate called after throwing an instance of 'int'

1

Hi, I get this error on 180,000 sequences that are around 500-5000bp long coming from PacBio Iso-Seq data. Any ideas? ``` avg length: 2199 Recommended K: 5 Reading in sequences...

Too many sequences below identity

5

Hi again, I tried running MeShClust on 500 sequences that I simulated, all of length ~900nucleotides with most of the sequences highly similar (edit distances 1-20bp). A small portion of...

Replacing isONclust with isONclust3 and corresponding parameters here: https://github.com/aljpetri/isONform/blob/master/isON_pipeline.sh We should use the (non default?) parameter --noncanonical so that output is still in same orientation for isONcorrect and isONform.

Strobealigns mapping-only accuracy in pared-end mode is worse than in single-end mode compared to minimap2 (See fig 2 in https://www.biorxiv.org/content/10.1101/2024.10.29.620855v1). Specifically, we produce higher accuracy mappings for short SE reads...