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  • Multiple whole genomes alignment

    Hello,
    I'm a newbie
    I have to align 5 whole chloroplast genomes de novo assembled with Soap2Denovo.
    Each genome is a multifasta file with both contigs and scaffolds.
    Some softwares needs to have for each genome a fasta file with only one sequence: can i obtain a fasta file with only one sequence merging alle scaffolds and contings?
    Thanks

  • #2
    You can do that, but the result would be junk, so I don't recommend it. It's not entirely clear to me what you are trying to accomplish, though.

    Comment


    • #3
      Originally posted by Brian Bushnell View Post
      You can do that, but the result would be junk, so I don't recommend it. It's not entirely clear to me what you are trying to accomplish, though.

      I have 5 chloroplast genomes of close related species and i have to align to a reference genome to find private Snp' in each genome.
      My aim is to find a set of snp in genomes that discriminates between species.

      Comment


      • #4
        OK, you can do that by aligning the chloroplast genomes to the reference without merging anything. For example, with BBMap:

        bbmap.sh ref=reference.fasta

        bbmap.sh in=chloro1.fasta out=chloro1.sam
        bbmap.sh in=chloro2.fasta out=chloro2.sam
        ...etc.

        Then you can call SNPs with samtools or something, with respect to coordinates on the reference.

        Comment


        • #5
          You can use MUMmer, it allows to compare draft genomes in multifasta format. There is also a pipeline with MUMmer to identify SNPs.

          Check the manual ----> http://mummer.sourceforge.net/manual/#aligningdraft

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