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  • #16
    You could also use 454's own mapper, gsMapper (runMapping), freely available through the 454 website (although closed-source). It is of course fully aware of the 454 error model and can generate BAM files, predict transcripts, as well as call SNPS. See http://454.com/contact-us/software-request.asp

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    • #17
      If you are annotating a genome and not just mapping I would strongly suggest the following
      - gmap (gives nice GFF3 output)
      - est2genome

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