rapid sample screening for shotgun DNA sequencing data sets
Project description
chill-filter: Rapid sample screening for shotgun sequencing data
Quickstart for the Web site:
- Clone the repo:
git clone https://github.com/dib-lab/chill-filter
cd chill-filter/
- Install flask, sourmash_plugin_branchwater, pandas, and snakemake.
conda env create -f environment.yml -n chill
conda activate chill
- Download the databases from the Open Science Framework project, and unpack them into
prepare-db/outputs/.
curl -JLO https://osf.io/download/bzu3v/
unzip -d prepare-db/ -nu chill-filter-db-0.2.zip
- 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)
- Run
chill_filter_web:
mkdir -p /tmp/chill
python -m chill_filter_web -p 5000
This will start a server at http://localhost:5000/
- Try uploading some FASTQ or FASTA files, or checkout the examples!
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