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Old 01-04-2013, 02:55 PM   #1
Location: CA

Join Date: May 2011
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Default Alinger for Ion PGM/Protn


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,
nguyendofx is offline   Reply With Quote
Old 01-07-2013, 07:24 AM   #2
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BWA works well, but I don't know of a good comparison of the aligners.
krobison is offline   Reply With Quote
Old 01-07-2013, 08:02 AM   #3
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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_bello is offline   Reply With Quote
Old 10-31-2013, 08:49 AM   #4
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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,
Saragh is offline   Reply With Quote

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