Read recuitment: promer and artemis

Question

[fhsantanna]

Hi,

I would like to do a read recruitment with a reference genome using the promer (mummer) software. However, I would like to use Artemis software to visualize the output, since it is easier to manipulate the figure with it than with the mummerplot.

I understood that the BAM file type (readable by Artemis) allows the mapping of reads on a reference genome. Is there a way to convert the promer output to BAM file type?

If it is not possible, do you know a better plot software to visualize the promer output?

Thanks in advance.

[fhsantanna]

I found bowtie2. I think it will do what I want.