Bhattlab workflows

Computational workflows for metagenomics tasks, packaged with Snakemake and singularity

Table of contents

1. Setup
2. Running a workflow
3. Available workflows
   • Preprocessing metagenomic data
   • Metagenomic Assembly
   • Metagenomic Binning
   • Metagenomic classification with Kraken2
   • Sourmash read comparison
   • Download SRA data
   • Comparative microbial genomics pipelines

Quickstart

snakemake --configfile config_preprocessing.yaml \
--snakefile ~/projects/bhattlab_workflows/preprocessing/preprocessing.snakefile \
--profile scg --jobs 100 --use-singularity \
--singularity-args '--bind /labs/,/oak/,/home/'