Using long reads to find a combination of mutations

Question

[eayasi]

Does anyone know of a way to quantify multiple connected mutations on single reads? I am trying to use my nanopore reads to see if specific combinations stand out. The reads are pretty noisy and doing it by hand seems tedious!

[WouterDeCoster]

So you want to phase your variants?

I think WhatsHap does what you need.

[eayasi]

This is on the right track of what I want to do. I forgot to mention I am not working with a diploid genome, but a plasmid library. I am not sure if this program will give me the data I am looking for, but I will test it out.

Answer 1

[colindaven]

Whatshap or Phaser https://github.com/secastel/phaser are on the right track here.

However I think these problems a) only work with maximal diploid ploidy and b) will struggle with nanopore reads.

I would first correct the reads by running canu on them, then use the resultant corrected fastq for further analysis.

Good luck