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Update README and project urls
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jlumpe committed Aug 17, 2022
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30 changes: 13 additions & 17 deletions README.md
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# GAMBIT

[![Build Status](https://github.com/hesslab-gambit/gambit/actions/workflows/ci.yml/badge.svg)](https://github.com/hesslab-gambit/gambit/actions/workflows/ci.yml)
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[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/hesslab-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.

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).

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.


Expand All @@ -19,7 +20,7 @@ detailed information on the tool and how to use it.
Install the Python library from Bioconda:

```
conda install -c bioconda hesslab-gambit
conda install -c bioconda gambit
```

Then download the reference database files and place them in a directory of your choice:
Expand All @@ -32,20 +33,15 @@ Then download the reference database files and place them in a directory of your

## Usage

gambit [-d DB_DIR] query [-f {csv|json}] [-o OUTFILE] GENOMES*
gambit [-d /path/to/database/] query [-o results.csv] genome1.fasta genome2.fasta ...

* `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.

See the documentation for additional details on the command line interface and description of the output.


## Contact

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]).
2 changes: 1 addition & 1 deletion docs/source/install.rst
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Expand Up @@ -8,7 +8,7 @@ Install from bioconda
The recommended way to install the tool is through the conda package manager (available
`here <https://docs.conda.io/en/latest/miniconda.html>`_)::

conda install -c bioconda hesslab-gambit
conda install -c bioconda gambit


Install from source
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4 changes: 2 additions & 2 deletions setup.cfg
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Expand Up @@ -4,7 +4,7 @@ description = Genomic Approximation Method for Bacterial Identification and Trac
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.


# Flake8 settings
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