Closing gaps

[memartin5]

Hello!
I would like to finish a bacterial genome of about 3millions bp. I have got two different results of the same genome from SOLID and Illumina sequencing. From Illumina I got about 25 contigs so I would like to close the gaps between them by aligning the contigs I obtained from the SOLID sequencing, from which I got many more contigs and also shorter ones.
Could you please suggest me an easy way to do that?
I tried with Mauve, I got the alignment but apparently the software eliminates the gaps so I can only see the contigs sequences.
I tried to do that with iMAGE software and Cap3 but I couldn't find any accessible usermanual.
Also I don't have Linux, but I'm working on a MacOS 10.8

thank you!

[GenoMax]

I tried to do that with iMAGE software and Cap3 but I couldn't find any accessible usermanual.
Also I don't have Linux, but I'm working on a MacOS 10.8

thank you!

Cap3 user manual: http://computing.bio.cam.ac.uk/local/doc/cap3.txt

You have OS X which is a BSD compliant unix operating system so pretty much anything you can do on linux you should be able to do with OS X.

Do you have a closely related genome available? Have you tried to use that with Mauve to see how complete your assembly looks? There may be some real gaps in your sequencing that may prevent you from getting a "finished" genome.

[memartin5]

I did not used a reference genome in Mauve, but just the two I had. And when I got the alignment I couldn't see any gaps apparently cause I guess Mauve automaticly delete them and do not consider them.
But I will definitely try to add another sequence, such as, a complete ref genome to see how it changes.

I am now looking at Geneious, hope it works for this aim!