brianchirn / bhattlab_workflows

Computational workflows for metagenomics tasks, by the Bhatt lab

Bhattlab workflows

Computational workflows for metagenomics tasks, packaged with Snakemake, Singularity and Conda.

Table of contents

1. Setup
2. Running a workflow
3. Available workflows
   • Preprocessing metagenomic data
   • Metagenomic Assembly
   • Metagenomic Binning
   • DeReplication of binned genomes
   • inStrain strain-diversity aware comparison of samples
   • Metagenomic classification with Kraken2
   • Sourmash read comparison
   • Download SRA data
   • ARG detection with RGI
   • Viral contig prediction
   • Comparative microbial genomics pipelines
   • MetaRibo-Seq

Quickstart

If you're in the Bhatt lab and working on SCG, this command is an example of how to run the workflows. Other users will need to change these options (see Running a workflow)

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

Important after running the preprocessing or assembly pipelines, run the cleanup rule in the snakefile. This will delete all the unnecessary files and save us space on SCG!

snakemake cleanup -s PATH/TO/SNAKEFILE --configfile YOUR_CONFIGFILE.yaml

You can also remove the .snakemake folder, which only contains metadata and cache from the run.

rm -rf .snakemake