Software - CSibelia
You have assembled the genomes, that's great!
C-Sibelia will help you in the next step: Comparing assemblies to a reference genome. As a result, you will get:
- A VCF file that describes all the found variants
- A circos picture visualizes all rearrangements
For your convenience, C-Sibelia also annotates and predicts the effects of these variants on genes using snpEff.
News: C-Sibelia is published in F1000Research.
If you use C-Sibelia, please cite: Minkin I, Pham H, Starostina E, Nikolay Vyahhi, and Son Pham (2013) "C-Sibelia: an easy-to-use and highly accurate tool for bacterial genome comparison", F1000Research 2013, 2:258.