Is Unicycler the best option for hybrid genome assembly?

• Scoary

  2 137 10.0 Python

  Pan-genome wide association studies

BONUS: I was planning on using Scoary (https://github.com/AdmiralenOla/Scoary) together with some Virulence data I have to look for some candidates. Any suggestion of alternative ways to identify virulence factors in these genomes?

• merqury

  3 258 6.4 Shell

  k-mer based assembly evaluation

  

Yeah, Unicycler is solid. iirc Unicycler v5.0+ removes Pilon, so you'll still want to polish your final assembly with your short reads. I like using QV as a quick way to see if I should polish more or not.

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• Perfect-bacterial-genome-tutorial

  2 104 4.5 Python

You should read this https://github.com/rrwick/Perfect-bacterial-genome-tutorial

• plassembler

  2 45 9.1 Python

  Program to quickly and accurately assemble plasmids in hybrid and long-only sequenced bacterial isolates

And a bit of a self plug, but you want to look at getting plasmids try this (it’s a work in progress but hopefully should work) https://github.com/gbouras13/plassembler

Suggest a related project