We built a new tool for disentangling local haplotypes from long-read sequencing: check out devider! https://github.com/bluenote-1577/devider
https://www.biorxiv.org/content/10.1101/2024.11.05.621838v1
1/5
https://www.biorxiv.org/content/10.1101/2024.11.05.621838v1
1/5
Comments
Main points:
(1) Works best with sequence length ~= read length
(2) Does not require prior knowledge of # of haplotypes (can be many!)
(3) Extremely fast (> 20,000x coverage is ok!)
(4) Requires reference
2/5
Technique inspired by a great paper from Zhou et al. for diploid haplotyping (https://www.nature.com/articles/s41467-024-47562-4)
3/5
We applied devider to a bovine gut metagenome enriched for AMR... and we found lots of interesting mosaic haplotypes. See the recombination blocks in the image (found by GARD).
4/5
Christina Boucher (https://www.christinaboucher.com),
Yun William Yu (https://yunwilliamyu.net/content/page...),
Noelle Noyes (https://www.thenoyeslab.org/people),
Heng Li (https://hlilab.github.io).
This project started from a random conversation at ISMB 2024 -- ended up with great collaboration!
5/5