GeneHunter

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. For details see LICENSE.

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]