Generating base quality information after sequence improvement

[KanyeDidIt]

Hi all,

We've tried using IMAGE2 for closing gaps on an assembly and so far have got very impressive results with respect to closing gaps and also improving contig stats.

I just wanted to know if there's any way to generate base quality files for the newly improved fasta file that is generated IMAGE?

Thanks!

https://sourceforge.net/apps/mediawiki/image2/index.php?title=Main_Page

[andreitudor]

I am interested in IMAGE2, as I have some sequences on which I need to close the gaps. The question I have is does it work on 454 data or only on Illumina?

[KanyeDidIt]

You normally need fastq reads and a fasta sequence to run IMAGE2.

[andreitudor]

I have the contigs assembled from the 454 data. Would that be ok?

[KanyeDidIt]

Yes if you also have illumina reads to align them to.

http://genomebiology.com/2010/11/4/R41

That's the paper on IMAGE2, it should help.

[andreitudor]

Thanks for the link. I do not have illumina reads. Only 454.