GULL

A tool for measuring relative similarity between non-assembled genomic sequences without supervision

Introduction

What is GULL ?

GULL is a tool for measuring relative similarity between non-assembled genomic sequences without supervision. The method is based on the relative information contained across the sequences, estimated by compression technology. All the sequences migth not be aligned or assembled!

It answers the following questions:

How do I get GULL ?

Clone our repository and run CMake command:
git clone https://github.com/pratas/GULL.git
cd GULL/src/
cmake .
make
Alternatively to CMake, run:
git clone https://github.com/pratas/GULL.git
cd GULL/src/
cp Makefile.nix Makefile
make

Usage

To see the possible options type
./GULL-map
./GULL-visual
or
./GULL-map -h
./GULL-visual -h
These will print the parameters that are needed to run both tools.
For GULL-map:
Usage: GULL-map [OPTION]... [FILE1]:[FILE2]:...
A tool for measuring relative similarity between 
non-assembled genomic sequences without supervision.  

Non-mandatory arguments:

  -h                       give this help,
  -V                       display version number,
  -v                       verbose mode (more information),
  -s                       how compression levels,
  -l <level>               compression level [1;30],
  -n <nThreads>            number of threads,
  -x <FILE>                similarity matrix filename,
  -o <FILE>                labels filename,

Mandatory arguments:

  <FILE>:<FILE>:<...>      input files (last arguments).
                           Use ":" for file splitting.

Report bugs to <{pratas,raquelsilva,ap,pjf}@ua.pt>.

For GULL-visual:
Usage: GULL-visual [OPTION]... [FILE]
A visual heatmap builder for any similarity matrix.

Non-mandatory arguments:

  -h                       give this help,
  -V                       display version number,
  -v                       verbose mode (more information),
  -w                       square width (for each value),
  -a                       square inter-space (between each value),
  -s                       index color start,
  -r                       index color rotations,
  -u                       color hue,
  -g                       color gamma,
  -l <FILE>                labels filename,
  -x <FILE>                heatmap filename,

Mandatory arguments:

  <FILE>                   input matrix file (last argument).

Report bugs to <{pratas,raquelsilva,ap,pjf}@ua.pt>.

Example

The following map shows and example while measuring relative similarity between human (HS), chimpanzee (PT) and gorilla (GG) chromosome sequences, including the unplaced (UP), the unlocalized (UL) and the mitocondrial (MT) sequences.

GULL-EXAMPLE

License

GPL v3. For more information see LICENSE file or visit
http://www.gnu.org/licenses/gpl-3.0.html