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chill-filter: Rapid sample screening for shotgun sequencing data

Quickstart for the Web site:

  1. Clone the repo:
git clone https://github.com/dib-lab/chill-filter
cd chill-filter/
  1. Install flask, sourmash_plugin_branchwater, pandas, and snakemake.
conda env create -f environment.yml -n chill
conda activate chill
  1. Download the databases from the Open Science Framework project, and unpack them into prepare-db/outputs/.
curl -JLO https://osf.io/download/5fw2v/
unzip -d prepare-db/ -nu chill-filter-db-0.4.zip
  1. Run snakemake in the sample-db/ directory to index the databases. It should take a few minutes at most.
(cd prepare-db && snakemake -j 1 -p)
  1. Run chill_filter_web:
mkdir -p /tmp/chill
python -m chill_filter_web -p 5000

This will start a server at http://localhost:5000/

  1. Try uploading some FASTQ or FASTA files, or check out the examples!