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  • Genome alignments

    Hello! My question is on how to make a "fake" reference genome from a set of contigs. I have the following data available:

    -Assembled contigs from my species (from genomic data, but I only have the contigs)
    -A reference genome (different species)
    -Linkage maps for both

    I would like to make an alignment between the contigs from my species and the reference, then concatenate the contigs from my species into a fake genome based on the order in the reference and/or linkage maps. The contigs are long (several kb), and I expect there to be many gaps due to introns, repeats, etc.

    Any suggestions for where to start? Thanks!

  • #2
    Take a look at Mummer for making the alignments.

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    • #3
      For mammalian genomes, bwa-sw.

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