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  • Daniel Fernandez
    replied
    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.

    Leave a comment:


  • sklages
    replied
    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).

    Leave a comment:


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

    Leave a comment:


  • Daniel Fernandez
    started a topic Assembly with Reference Sequence

    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.

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