EAGLE is a program to map minimal Relative Absent Words (mRAWs). EAGLE identifies and localizes the mRAWs contained in a range size of k-mers, running on a command-line environment with multi-threads to minimize computation times. It contains extensions to estimate CG distributions and create automatic plots (Gnuplot). It works on FASTA data without size limitations.
CMake must be installed to compile EAGLE. CMake can be downloaded from the CMake webpage (http://www.cmake.org/) or by an appropriate packet manager. The following instructions show the procedure to install and compile EAGLE manually:
git clone https://github.com/pratas/eagle.git
cd eagle/src/
cmake .
make
Run EAGLE using:
./EAGLE -v -t -min 11 -max 14 -p -r Human.fna SARS-CoV-2.fa
To see the possible options type
./EAGLE
or
./EAGLE -h
These will print the following options:
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NAME
EAGLE v2.1 2015-2020
Efficient computation of minimal Relative Absent Words (mRAWs).
AUTHORS
D. Pratas (<last_name>@ua.pt).
SYNOPSIS
./EAGLE [OPTION]... [FILE] [FILE]
SAMPLE
Run: ./EAGLE -v -F -i -min 11 -max 16 human.fa SARS-CoV2.fa
DESCRIPTION
Localization and quantification of minimal Relative Absent Words.
-h, --help
usage guide (help menu).
-V, --version
display program and version information.
-f, --force
force mode. Overwrites old files.
-v, --verbose
verbose mode (more information).
-t, --threads
does NOT use threads if flag is set (slower).
-i, --ignore-ir
does NOT use inverted repeats if flag is set.
-o, --stdout
write to standard output.
-p, --plots
print Shell code to generate plots (gnuplot).
-min [NUMBER], --minimum [NUMBER]
k-mer minimum size (usually 10).
-max [NUMBER], --maximum [NUMBER]
k-mer maximum size (usually 16).
[FILE]
Input FASTA reference (e.g. human genome) -- MANDATORY.
The content of this file will be loaded in the models.
[FILE]
Input FASTA target (e.g. multi SARS-CoV2) -- MANDATORY.
The mRAWs will be mapped on the content of this file.
COPYRIGHT
Copyright (C) 2015-2020, IEETA/DETI, University of Aveiro.
This is a Free software, under GPLv3. You may redistribute
copies of it under the terms of the GNU - General Public
License v3 <http://www.gnu.org/licenses/gpl.html>. There
is NOT ANY WARRANTY, to the extent permitted by law.
Version 2.1:
- Article under Review
version 1.0:
- R. M. Silva, D. Pratas, L. Castro, A. J. Pinho & P. J. S. G. Ferreira. Bioinformatics (2015): btv189. URL.
For any issue let us know at issues link.
GPL v3.
For more information:
http://www.gnu.org/licenses/gpl-3.0.html