chill-filter 0.1

rapid sample screening for shotgun DNA sequencing data sets

chill-filter:Rapid sample screening for shotgun sequencing data

Quickstart for the Web server:

0. 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

2. Download the databases from the Open Science Framework project, and unpack them into prepare-db/outputs/.

curl -JLO https://osf.io/download/pwfn8/
mkdir -p prepare-db/outputs/
unzip -d prepare-db/outputs/ -nu chill-filter-db-0.1.zip

3. 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)

4. Run chill_filter_web:

mkdir -p /tmp/chill
python -m chill_filter_web

This will start a server at http://localhost:5000/, by default.

5. Try uploading k=51, scaled=100_000 sketches!

e.g. there are a bunch in examples/ to try.