Using long reads to find a combination of mutations
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!
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colindaven
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eayasi •
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eayasi •
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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
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So you want to phase your variants?
I think WhatsHap does what you need.
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.