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  • Scaffolding and assembly quality evaluation/visualisation tools?

    Hi All,

    I am working with de-novo seq of fungal genomes. Sometimes I am really frustrating with different assemblies/scaffolding structures I am able to get from the same datasets just varying assembly parameters. It is especially important for large clusters of genes (up to 100-200kb), where I have to be very confident with order/orientation of genes.

    What I am looking for: the software to verify (probably just visually) the quality of linking contigs into scaffolds, based on paired/mate reads mapping and quality info.

    The options I've found now are:
    - Tablet
    - Hawkeye and AMOS

    Are there somebody using these? Any other suggestions?
    Thank you

  • #2
    The tool 'Bandage' can visualize assemblies from SPAdes using the fastG format it produces. You can load the results of the final scaffolds or the intermediate K-mer contigs. Also, you can BLAST sequences (e.g. gene sequences) to see where it sits within the assembly graph.

    The tool is available here;



    Boetsie

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    • #3
      You can try some of the tools which evaluate the quality of the mapping like CGAL or RSEM-EVAL. Maybe these can give you an idea which assembly is better.

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