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Old 10-03-2014, 05:47 PM   #1
Antony03
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Location: Canada, Quebec

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Default How to correct a ref seq using Illumina

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
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Old 10-06-2014, 11:13 AM   #2
flxlex
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Have a look at pilon: http://www.broadinstitute.org/software/pilon/
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