Under the hood¶

Snakemake, environments and containers¶

Snakemake¶

Conda environments¶

Singularity containers¶

Input output definition¶

Input¶

A set of Python functions is run at each execution of the RSP4ABM to match sequencing read files to each sample.

As exposed in the sample selection section of the Pipeline execution page, RSP4ABM can accept either local or SRA-hosted read files.

Local reads¶

In the case of locally stored

SRA reads¶

Output¶

Logging and traceability¶

Snakemake logs¶

RSP4ABM logs¶

Sequencing reads QC¶

Denoising¶

Vsearch (OTU clustering)¶

PANDAseq¶

Vsearch¶

DADA2 (ASV denoising)¶

cutadapt¶

DADA2¶

Taxonomic assignment¶

reference database¶

classifiers¶

Post-processing¶

Taxonomic filtering¶

Rarefaction¶

Phylogenetic tree generation¶

Taxonomic collapsing¶

Normalization and abundance-based filtering¶

Exports¶

Fromatting¶

Wide to long melting¶

transpose_and_meta_count_table¶

Qiime2 formats¶

Picrust2¶