looking for reference-guided genome assembly tools

[capricy]

Hello, there,

I got the illumina data from two E coli isolate genomic DNA and try to do the assembly. There are many de novo assemblers around. I just wonder if there are any tools for reference-based assembler since this bacterium has reference deposit.

Thank you very much for any input!

C

[mastal]

Velvet has options for reference-guided assembly. See the velvet webpage. I think the module for assembly using a reference is called Columbus, and there is a manual.

https://www.ebi.ac.uk/~zerbino/velvet

https://www.ebi.ac.uk/~zerbino/velvet/Columbus_manual.pdf

I'm pretty sure you can also do reference-based assembly with Mira.

[capricy]

Thank you so much for the information. I will explore those methods.

C.