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# GAMBIT | ||
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[![Build Status](https://github.com/hesslab-gambit/gambit/actions/workflows/ci.yml/badge.svg)](https://github.com/hesslab-gambit/gambit/actions/workflows/ci.yml) | ||
[![Documentation Status](https://readthedocs.org/projects/hesslab-gambit/badge/?version=latest)](https://hesslab-gambit.readthedocs.io/en/latest/?badge=latest) | ||
[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/hesslab-gambit/README.html) | ||
[![Build Status](https://github.com/jlumpe/gambit/actions/workflows/ci.yml/badge.svg)](https://github.com/jlumpe/gambit/actions/workflows/ci.yml) | ||
[![Documentation Status](https://readthedocs.org/projects/gambit-genomics/badge/?version=latest)](https://gambit-genomics.readthedocs.io/en/latest/?badge=latest) | ||
[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/gambit/README.html) | ||
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GAMBIT (Genomic Approximation Method for Bacterial Identification and Tracking) is a tool for rapid taxonomic identification of microbial pathogens. | ||
It uses an extremely efficient genomic distance metric along with a curated database of approximately 50,000 reference genomes (derived from NCBI | ||
[RefSeq](https://www.ncbi.nlm.nih.gov/refseq/)) to identify query genomes within seconds. | ||
[RefSeq](https://www.ncbi.nlm.nih.gov/refseq/)) to identify unknown bacterial genomes within seconds. | ||
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Developed by Jared Lumpe in collaboration with the David Hess lab at Santa Clara University. Publication coming soon. | ||
Developed by Jared Lumpe in collaboration with the Nevada State Public Health Lab and the David Hess lab at Santa Clara University. | ||
Preprint available [here](https://www.biorxiv.org/content/10.1101/2022.06.14.496173v1). | ||
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See the [documentation](https://hesslab-gambit.readthedocs.io/en/stable) for more | ||
See the [documentation](https://gambit-genomics.readthedocs.io/en/latest) for more | ||
detailed information on the tool and how to use it. | ||
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Install the Python library from Bioconda: | ||
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``` | ||
conda install -c bioconda hesslab-gambit | ||
conda install -c bioconda gambit | ||
``` | ||
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Then download the reference database files and place them in a directory of your choice: | ||
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## Usage | ||
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gambit [-d DB_DIR] query [-f {csv|json}] [-o OUTFILE] GENOMES* | ||
gambit [-d /path/to/database/] query [-o results.csv] genome1.fasta genome2.fasta ... | ||
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* `GENOMES` are one or more files containing query genomes. Currently only FASTA format is supported. | ||
They must be assembled but may consist of multiple contigs. Support for unassembled raw reads in | ||
FASTQ format is in development. | ||
* `DB_DIR` is the directory containing the database files. Alternatively you may set the | ||
`GAMBIT_DB_PATH` environment variable in order to avoid typing this each time. | ||
* `OUTFILE` is the file to write results to. | ||
* `-f` sets the output format (defaults to `csv`). | ||
Positional arguments are one or more FASTA files containing query genome assemblies. You must | ||
provide the path to the directory containing the database files using either the `-d` option | ||
(*before* the `query` subcommand) or by setting`GAMBIT_DB_PATH` environment variable. | ||
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See the documentation for additional details on the command line interface and description of the output. | ||
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## Contact | ||
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For questions regarding usage of the software itself, please contact Jared Lumpe at [[email protected]](mailto:[email protected]). | ||
All other questions should be directed to David Hess at [[email protected]](mailto:[email protected]). | ||
Please contact Jared Lumpe at [[email protected]](mailto:[email protected]). |
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version = attr: gambit.__version__ | ||
author = Jared Lumpe | ||
author_email = [email protected] | ||
url = http://github.com/hesslab-gambit/gambit | ||
url = http://github.com/jlumpe/gambit | ||
license = AGPL-3.0-or-later | ||
license_file = LICENSE | ||
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# Custom markers | ||
markers = | ||
testdb_nqueries: number of query files from testdb_nqueries to use when testing CLI. | ||
testdb_nqueries: number of query files from test database to use when testing CLI. | ||
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# Flake8 settings | ||
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