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Metagenomic Taxonomic Profiling (beginner)

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  • Metagenomic Taxonomic Profiling (beginner)

    Hello, a little bit about myself. I'm a first year bioinformatic grad student who somehow got himself into a mock metagenomic project (there will be an actual project in half a year). I have no prior experience with metagenomics side and there are no courses being offered in my university that covers the basic of metagenomic.

    For the project, I am expected to 1) find and download human metagenomic data (raw reads), 2) perform taxonomic assignment (taxonomic profiling, etc), and 3) perform comparative metagenomic is possible.

    I somehow managed to download files (in fastq.gz format) from the human microbiome project database. I vaguely know I should use software such as Kraken but I honestly have no clue (and no one to ask in rl) who should I even begin. If anyone can point me towards the right direction or leave hints, it will be a life saver.