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Old 04-10-2012, 01:02 AM   #1
RocheKermit
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Location: Luxembourg

Join Date: Nov 2011
Posts: 15
Default Quality score at the single base level in a multiple alignment

Dear all,
In a 454 amplicon experiment, we've defined a particular population of reads. We would like to have a view of these reads with their quality at the single base level. I mean that we would like first to align them together and next to visualize the quality at each nucleotide position. Ideally the overall quality at a specific position and also the quality of one read at a specific position.
AVA doesn't propose that, it can only show the flowgrams.
In Jalview I wasn't able to add the information related to the quality, that tool is not designed for that.
IGV is better designed to map over the genome, which is not my kind of sequences (virus).

Does anybody know a tool able to show such information?

Thanks a lot!
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