How to correct a ref seq using Illumina

[Antony03]

Dears colleagues,

Last year, I made the assembly of a complete bacterial genome using 454 sequencing reads. However, as you probably know, 454 technology is prone to frameshift. Consequently, I sequenced the strain DNA using Illumina MiSeq. Is there a software to correct reference genome (in fasta) with illumina reads? I know there are iCORN and iCORN 2, unfortunately I have experimented some problems with them.

Thank!

Antony

[flxlex]

Have a look at pilon: http://www.broadinstitute.org/software/pilon/