Using fly to detect contamination in a pure culture?

mikolmogorov / Flye

De novo assembler for single molecule sequencing reads using repeat graphs

Other

743 stars 164 forks source link

Using fly to detect contamination in a pure culture? #668

Closed Ge0rges closed 4 months ago

Ge0rges commented 5 months ago

Hello,

I am sequencing what I think to be a pure culture on Nanopore. When I assemble using flye I get a circular genome or near circular genome.

However, I'd like to increase my confidence that the culture is not in fact a co-culture if two closely related bacteria.

I was wondering if using --meta would be recommended in this case to reveal this "hidden contamination"? Or if instead it would be more apt to use --keep-haplotypes?

Thank you for your advice.

mikolmogorov commented 4 months ago

I think --meta --keep-haplotypes is good and should reveal any possible structural variants (500bp+). We are also working on Strainy that can phase small variants if there are any: https://github.com/katerinakazantseva/stRainy