https://github.com/braintwister/genehunter

Identification of organisms from a stream of DNA sequences
https://github.com/braintwister/genehunter

dna-sequencing genome-analysis

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Identification of organisms from a stream of DNA sequences

• Host: GitHub
• URL: https://github.com/braintwister/genehunter
• Owner: BrainTwister
• License: mit
• Created: 2014-05-14T20:18:32.000Z (about 11 years ago)
• Default Branch: master
• Last Pushed: 2017-01-31T14:32:44.000Z (over 8 years ago)
• Last Synced: 2025-01-19T21:39:03.307Z (4 months ago)
• Topics: dna-sequencing, genome-analysis
• Language: C++
• Homepage:
• Size: 258 KB
• Stars: 3
• Watchers: 1
• Forks: 0
• Open Issues: 3
• Metadata Files:
  • Readme: README.md
  • License: LICENSE.md

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README

        
GeneHunter

==========

[![Build Status](https://travis-ci.org/BrainTwister/GeneHunter.png)](https://travis-ci.org/BrainTwister/GeneHunter)

[![Coverage Status](https://coveralls.io/repos/github/BrainTwister/GeneHunter/badge.svg?branch=master)](https://coveralls.io/github/BrainTwister/GeneHunter?branch=master)

[![Code Quality](https://landscape.io/github/BrainTwister/GeneHunter/master/landscape.svg)](https://landscape.io/github/BrainTwister/GeneHunter/master)



  



[![MIT](http://img.shields.io/badge/license-MIT-green.svg?style=flat)](http://opensource.org/licenses/MIT)

Identification of organisms from a stream of DNA sequences.

Copyright © 2013-2016 BrainTwister - All rights reserved.

GeneHunter is free software made available under the [MIT License](http://opensource.org/licenses/MIT). For details see [LICENSE](LICENSE.md).

Requirements

------------

- cmake (Version >= 3.0, http://www.cmake.org)

- Boost (Version >= 1.52, http://www.boost.org, modules: filesystem, iostreams, serialization, and system)

- MySQL

- gtest (optional)

- doxygen (optional)

For Ubuntu 14.04 please install following packages:

    sudo apt-get install cmake libboost-all-dev libgtest-dev doxygen mysql-client libmysqlclient-dev

Installation

------------

1) Get the source code using git:

    git clone https://github.com/BrainTwister/GeneHunter

  

2) Make build directory and change into it:

  

    mkdir GeneHunter/build

    cd GeneHunter/build

3) Generate Makefile using cmake:

    cmake ..

4) Compile:

    make -j 

5) Execute the Tests

    make test

6) Download Nucleotide database

    wget ftp://ftp.ncbi.nih.gov/blast/db/FASTA/nt.gz

7) Download and generate gene database

    wget ftp://ftp.ncbi.nlm.nih.gov/genbank/*.seq.gz

 

    CDSDatabaseBuilder [input-files]

8) Download and generate taxonomy database

    wget ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz

    wget ftp://ftp.ncbi.nih.gov/pub/taxonomy/gi_taxid_nucl.dmp.gz

    TaxonomyDatabaseBuilder [gi_taxid_nucl] [names] [nodes]

9) Edit and set environmental variables

    source ../settings/bashrc

Usage

-----

    GeneHunter [read-file] [description-file] [result-file] [nt-file]