search

gtonkinhill / fastbaps

A fast approximation to a Dirichlet Process Mixture model (DPM) for clustering genetic data
MIT License
58 stars 8 forks source link

Alignment tool #26

Closed jsgounot closed 4 months ago

jsgounot commented 4 months ago

Hi,

this issue is more related to your paper. I was curious how you aligned the sequences/genomes from your bacterial dataset. Do you have a recommended way to produce an alignment from a set of bacterial genomes before sending it fastbaps?

Thanks, JS

gtonkinhill commented 4 months ago

Hi,

I generally use Snippy. You could also take a look at SKA which uses a reference free based approach.

jsgounot commented 4 months ago

Hi,

I thought you were working with assemblies and not reads, my bad. Thanks for your recommendations.

JS