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  • eoh001
    Member
    • Mar 2011
    • 19
    #1

    need mapping solutions for 454 reads

    Hello
    I tried to map 454 reads with GS reference mapper.
    I want to map them with different algorithm.
    Could you recommed any software good for 454 reads?
    Thanks!!!!
    Tags: None
    • lukas1848
      Member
      • Jun 2011
      • 54
      #2
      You could try GMAP or bwa (with sw option set). Do you have PE or SE reads and do you have cDNA or genomic reads?

        Comment

        • ulz_peter
          Senior Member
          • Feb 2010
          • 219
          #3
          a very popular algorithm for 454 reads is SSAHA2

            Comment

            • KaiYe
              Senior Member
              • Jun 2009
              • 133
              #4
              a newer version of SSAHA2 is SMALT.

                Comment

                • adaptivegenome
                  Super Moderator
                  • Nov 2009
                  • 436
                  #5
                  SMALT and BWA-SW are good. We have had some improved results by splitting the reads at homopolymers.

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