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  • 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

  • #2
    BWA works well, but I don't know of a good comparison of the aligners.

    Comment


    • #3
      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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      • #4
        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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