Magma

Bioinformatics pipeline for processing 16S rRNA amplicon sequence data.

Pipeline

Custom parameters stored in config.yaml. See below for a description of the parameters.

Installation

To use: navigate to project directory. Clone this repository using the following:

git clone https://github.com/alanaschick/magma.git magma

Note: you need to have conda and snakemake installed locally in order to run this. See instructions below.

Executing

Step 1. Enter location of sequences and list of file names in config.yaml file.

Step 2. To execute:

Test the pipeline:

snakemake -np

Run the pipeline:

snakemake --use-conda

Remove Adapters

• This pipeline uses the cutadapt software to remove adapters from the raw sequence reads.

Filtering

• Remove low quality reads using dada2::filterAndTrim function.
• Check quality post filtering with fastqc and multiqc.

Dada2 Workflow

• Generate error model and denoise reads.
• De-replicate and infer sequence variants.
• Remove bimeras, assign taxonomy.
• Track reads throughout processing, print results to table.

Conda and Snakemake

To install conda, see the instructions here.

To install snakemake using conda, run the following line:

conda install -c bioconda -c conda-forge snakemake

See the snakemake installation instructions for further details.