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  • julien
    Junior Member
    • Nov 2009
    • 3
    #1

    Pileup to contig

    Hi,
    I was wondering if any of you know of, or have a script to go from a pileup to series of contigs? It seems like the easiest way to get contigs from a BWA alignment but maybe someone has a better solution ?

    Thank you !!!!!
    Tags: None
    • lh3
      Senior Member
      • Feb 2008
      • 686
      #2
      samtools.pl pileup2fq

        Comment

        • colindaven
          Senior Member
          • Oct 2008
          • 417
          #3
          Also try Galaxy

          Galaxy
          http://main.g2.bx.psu.edu/
          Galaxy is a community-driven web-based analysis platform for life science research.


          They have a couple of pileup tools in the samtools section on NGS data.

          Works nicely

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