/amplicon-qiime2

Snakemake pipeline for amplicon data, based mainly on qiime2

Primary LanguagePythonMIT LicenseMIT

Amplicon pipeline

This pipeline is based mainly in QIIME2, using dada2 as denoiser and q2-sepp plugin to build a phylogenetic tree. sepp implements an algorithm to insert sequences into an existing (large) phylogeny (greengenes by default). This pipeline also implements an alternative workflow for reconstructing a de novo phylogeny using mafft and fasttree, which is much lighter in terms of computing resources than sepp.

For diversity, produces multiple alpha and beta metrics. Furthermore, it produces a taxonomy analysis based in a scikit-learn classifier specially trained for the specific type of amplicon (16S rRNA hyper-variable V4 region), generating interactive bar plots and a krona plot.

For differential abundance analysis, It runs "analysis of composition of microbiomes", ANCOM, using its qiime plugin.

Run the first part of the pipeline, needed to select certain parameters used afterwards

snakemake -pr --forceall demux_summary -j $Core_Number

        count   jobs
        16      cutadapt_pe
        1       demux_summary
        1       make_samples
        1       qiime_import

Run the whole pipeline

snakemake -pr -j $Core_Number

Pipeline's directed acyclic graph

DAG