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  • Alignment Visualization

    I am looking for a way to align contigs from a de novo assembly against a reference genome and visualize which parts of the genome are covered. Any recommendations?

    Thanks

  • #2
    I really like Tablet (http://bioinformatics.oxfordjournals...t/btp666v1.pdf) as a genome viewer. I believe it supports ACE, AFG, MAQ, SOAP and SAM formats.

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    • #3
      But Tablet is for viewing individual contigs from assemblies on their own (looking at the reads within a contig).

      The question was about comparing the contigs of an assembly against a reference genome. This has similarities to comparing different genomes... maybe ACT (the Artemis Comparison Tool) would be suitable?
      http://www.sanger.ac.uk/resources/software/act/

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      • #4
        We used BLASTn to map ca 2000 contigs against various references.
        Visualisation of contig position and the annotated genes in that region was with the R package GenomeGraphs.

        I would really recommend this and can send an example script if you pm me with your email address.

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        • #5
          What is your average contig length? For contigs assembled from short reads I have been using " bwa bwasw"

          It natively produces SAM format which your can convert to BAM and directly view in Tablet/IGV

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          • #6
            mummer may be best option

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