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  • #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
  • #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?

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    • #3
      a very popular algorithm for 454 reads is SSAHA2

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      • #4
        a newer version of SSAHA2 is SMALT.

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        • #5
          SMALT and BWA-SW are good. We have had some improved results by splitting the reads at homopolymers.

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