Mauve Genome Alignment software

Question

[Rahul]

Hello,

I am using Mauve for computing genome alignment with help of reference plant genome,but I am not getting any results.Mauve console window only displaying "Gap found". I have already done with velveth and velvetg. My data is generated from fosmid library (plant partial genomic library). Can I get any suggestion for doing data analysis after velvet?

Answer 1

[arnstrm]

Assuming you completed a de novo assembly, you can probably use some assembly improvement programs that can pull together some scaffolds. Check out PAGIT, PILON and various other tools. Using many extra scaffolding program doesn't hurt either (SSPACE, Scaffold_builder etc.). You can also try MUMmer for aligning it to the closest reference genome and manually assembling the scaffold order. Lastly, you should probably try different assemblers or different settings (like kmer) of an assembly programs to generate different versions of the assembly and merge them together to get a good assembly.