Alinger for Ion PGM/Protn

[nguyendofx]

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

[krobison]

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

[bernardo_bello]

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

[Saragh]

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.