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/5fw2v/
unzip -d prepare-db/ -nu chill-filter-db-0.4.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 check out the examples!
Download files
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.
Source Distribution
chill_filter-0.4.0.tar.gz
(3.4 MB
view details)
Built Distribution
Filter files by name, interpreter, ABI, and platform.
If you're not sure about the file name format, learn more about wheel file names.
Copy a direct link to the current filters
File details
Details for the file chill_filter-0.4.0.tar.gz.
File metadata
- Download URL: chill_filter-0.4.0.tar.gz
- Upload date:
- Size: 3.4 MB
- Tags: Source
- Uploaded using Trusted Publishing? No
- Uploaded via: twine/6.0.1 CPython/3.11.6
File hashes
| Algorithm | Hash digest | |
|---|---|---|
| SHA256 |
33e38a6fb7011934f9261ba7cbe87dbbbf38856425ba2e88ff210f37ee7792db
|
|
| MD5 |
073e969d5ae0bebcec51a19d03c8efe2
|
|
| BLAKE2b-256 |
f7d6bda905bece6e1f55093c562892f29d617e40384cbd73e89da172daecce3f
|
File details
Details for the file chill_filter-0.4.0-py3-none-any.whl.
File metadata
- Download URL: chill_filter-0.4.0-py3-none-any.whl
- Upload date:
- Size: 3.4 MB
- Tags: Python 3
- Uploaded using Trusted Publishing? No
- Uploaded via: twine/6.0.1 CPython/3.11.6
File hashes
| Algorithm | Hash digest | |
|---|---|---|
| SHA256 |
41c2f2d1fd4edb9c1bf49580bd74a02953dc4e953426a25a985c7b9a2aff6ecc
|
|
| MD5 |
43a74e5aa5a3993fc44b2a8136909464
|
|
| BLAKE2b-256 |
841b7b8e4bbdd20a6c76ddd17fd70bcb6c6e3a3306636c1433beab97e357205d
|
