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  • The software for metagenomic DNA shotgun sequencing

    Hello,

    I have metagenomic DNA shotgun sequencing data now. Are there any suggested software for analyzing ? Thank you for help.

  • #2
    Here's a good guide on what you can do with your data:
    Metagenomics applies a suite of genomic technologies and bioinformatics tools to directly access the genetic content of entire communities of organisms. The field of metagenomics has been responsible for substantial advances in microbial ecology, evolution, and diversity over the past 5 to 10 years, and many research laboratories are actively engaged in it now. With the growing numbers of activities also comes a plethora of methodological knowledge and expertise that should guide future developments in the field. This review summarizes the current opinions in metagenomics, and provides practical guidance and advice on sample processing, sequencing technology, assembly, binning, annotation, experimental design, statistical analysis, data storage, and data sharing. As more metagenomic datasets are generated, the availability of standardized procedures and shared data storage and analysis becomes increasingly important to ensure that output of individual projects can be assessed and compared.



    In short, you can try aligning your reads to known databases like Genbank (bacteria, virus and phage nucleotide and protein sequences). There are some recent fast tools to do so like Kraken and PAUDA. You can try assembling your reads into genomes with different assembly tools like Ray, MetaVelvet, IDBA, SOAPdenovo and then annotating the contigs. Or you can do some database independent analysis with differential coverage binning, clustering with machine learning algorithms and such.

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    • #3
      Thank you for suggestions. I got many contigs from my sequencing data. Are there any suitable tools for doing gene predicting for these contigs.

      Comment


      • #4
        This paper and papers citing it might provide some ideas: http://genomebiology.com/2013/14/1/R2
        Last edited by nucacidhunter; 08-13-2014, 03:42 PM.

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