Diagram of QIIME 2 metagenomics workflow

Warning

Metagenomics analysis with QIIME 2 is in alpha release. This means that results you generate should be considered preliminary, and NOT PUBLICATION QUALITY. Additionally, interfaces are subject to change, and those changes may be backward incompatible (meaning that a command or file that works in one version of the QIIME 2 Shotgun Metagenomics distribution may not work in the next version of that distribution).

This is an initial mental model of what this workflow looks like as a mermaid flowchart. If a graph isn’t rendering below, you can copy/paste the code you see to the mermaid live editor.

flowchart TD;
    a("Demultiplex
       ideally and typically done by the sequencing center");
    b("Adapter removal
       ideally but never done by the sequencing center
       (`qiime cut-adapt`)");
    a-->b;
    b-->c("`qiime demux summarize`");
    c-->d("Merge paired end reads
          (`qiime vsearch merge-pairs`, optional)");
    d-->e("Host read removal
          (`qiime quality-control filter-reads`)");
    e-->f("Paired end and/or merged reads");
    f-->g("Assemble contigs");
    g-->h("Map reads to contigs");
    h-->i("Bin MAGs");
    i-->n("Dereplicate MAGs");
    f-->j("Taxonomy annotation");
    j-->k("Taxonomy feature table");
    k-->o("Host read removal again
          (`qiime taxa filter --p-include k__Bacteria,k__Archaea,k__Fungi,k__Virus --p-exclude p__Chordata ...`)")
    o-->p("Downstream diversity analyses");
    f-->l("Functional annotation");
    l-->m("Functional feature table");
    m-->p;
    g-->j;
    g-->l;
    n-->j;
    n-->l;