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  • Assembly with Reference Sequence

    Hi, anybody can tell me about one program to assembly with a reference sequence (in Linux)
    I use CAP3 but this can't use a reference sequence.

    Well I need assembly more than 300 million, so I prefer a command program like CAP3
    Or I can use other program (blast) to choose the best reads (less 500) and then assembly this hits with a reference sequences with a graphic program.

    I've been looking but no luck.

  • #2
    What is your sequencing platform? assuming illumina you can use Velvet's Columbus module as suggested by:

    Comment


    • #3
      Originally posted by Daniel Fernandez View Post
      Hi, anybody can tell me about one program to assembly with a reference sequence (in Linux)
      I use CAP3 but this can't use a reference sequence.

      Well I need assembly more than 300 million, so I prefer a command program like CAP3
      Or I can use other program (blast) to choose the best reads (less 500) and then assembly this hits with a reference sequences with a graphic program.

      I've been looking but no luck.
      Not much information you provide :-)
      type of input material? type of data? type of reference?

      Have a look at http://seqanswers.com/wiki/Software to get idea of what software might be doing the job for you. There are numerous mappers (assuming you refer to mappping).

      Comment


      • #4
        Well, this is the link, it is 454 (http://www.ncbi.nlm.nih.gov/sra/SRX172665).
        This genome is in SRA and I converted to fastq and then fasta. My reference sequences are genes in fasta.
        I'm trying with Velvet thanks for the recommendation, if anymore have other sugestion, thanks.

        Comment

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