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Old 01-04-2013, 03:55 PM   #1
nguyendofx
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Default Alinger for Ion PGM/Protn

Hello,

I use TMAP aligner for Ion PGM (200 - 400 bp reads long) short read currently. Does anyone know any other aligner can handle the Ion PGM/Proton reads? is there a comparison between aligners on Ion PGM reads?

Thank you very much,
Ng
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Old 01-07-2013, 08:24 AM   #2
krobison
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BWA works well, but I don't know of a good comparison of the aligners.
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Old 01-07-2013, 09:02 AM   #3
bernardo_bello
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The best you can do is to compare results between aligners. For Ion Torrent TMAP was the best for me. I discarded BWA and Bowtie.

Bernardo
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Old 10-31-2013, 09:49 AM   #4
Saragh
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Hi all,
Can anybody help me figure out best tools to identify different haplotypes for Ion PGM data. I have sequences of environmental samples and I would like to find out different haplotypes exist within each taxonomic group.
Thank you,
Sara.
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