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  • mapping of metagenomic data to multiple reference genomes

    Hi,

    I am trying to map metagenomic data to a set of more than a thousand genomes.
    I expect many of the reads not to align to anything as it is metagenomic data and there are many bugs out there that do not have a reference genome.

    I am not sure what would be the best alignment tool in this case. Was thinking about Bowtie2 but as far as I understand I will need to index each of the reference genomes separately and run each of my samples against each of the indexes.

    Any suggestions?

    Thanks,
    Marie

  • #2
    This depends on your specific goal. You can always just concatenate all the references together in a single file, and then index that, which would allow you to use any mapper, with a single pass. You'd have to ensure all of the scaffolds have unique names, though.

    Alternately, I have a program called BBSplit designed for mapping against multiple references simultaneously, for the purpose of binning reads - it outputs one file per reference, containing all of the reads that mapped best to that particular reference; in addition, it generates statistics about the fraction of reads that aligned to each, so you can estimate the composition of the community.

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