FALCON FALCON

A compression method  to infer metagenomic sample composition

Introduction

What is FALCON ?

FALCON is a compression method to infer metagenomic sample composition. FALCON looks for similarity between any genomic sequence (ACGTN), FASTA or FASTQ file, independently from the size, against any multi-FASTA database, such as the entire viral and bacterial NCBI database (scripts are available for multiple database downloads).

It answers the following questions:

How to get FALCON ?

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

How to run FALCON ?

Assuming that you have already a FASTQ sample (such as human) and a Viruses database (there are scripts to simply download it), type:
./FALCON -v -l 19 -t 50 human.fq Viruses.fa

Usage

To see the possible options of FALCON type
./FALCON
or
./FALCON -h
These will print the following options:
Usage: FALCON [OPTION]... [FILE1] [FILE2]
A compression-based method to infer metagenomic sample composition.

Non-mandatory arguments:

  -h                       give this help,
  -F                       force mode (overwrites top file),
  -V                       display version number,
  -v                       verbose mode (more information),
  -Z                       database local similarity,
  -s                       show compression levels,
  -l <level>               compression level [1;44],
  -p <sample>              subsampling (default: 1),
  -t <top>                 top of similarity (default: 20),
  -n <nThreads>            number of threads (default: 2),
  -x <FILE>                similarity top filename,
  -y <FILE>                local similarities filename,

Mandatory arguments:

  [FILE1]                  metagenomic filename (FASTA or FASTQ),
  [FILE2]                  database filename (FASTA or Multi-FASTA).

Report issues to <{pratas,ap,pjf,jmr}@ua.pt>.

Local detection

For local interactions detection and visualization the package provides FALCON-FILTER and FALCON-EYE.

Filtering

To see the possible options of FALCON-FILTER type
./FALCON-FILTER
or
./FALCON-FILTER -h
These will print the following options:
Usage: FALCON-FILTER [OPTION]... [FILE]
Filter and segment FALCON output.

Non-mandatory arguments:

  -h                       give this help,
  -F                       force mode (overwrites top file),
  -V                       display version number,
  -v                       verbose mode (more information),
  -s  <size>               filter window size,
  -w  <type>               filter window type,
  -x  <sampling>           filter window sampling,
  -sl <lower>              similarity lower bound,
  -su <upper>              similarity upper bound,
  -dl <lower>              size lower bound,
  -du <upper>              size upper bound,
  -t  <threshold>          threshold,
  -o  <FILE>               output filename,

Mandatory arguments:

  [FILE]                   profile filename (from FALCON),

Report issues to <{pratas,ap,pjf,jmr}@ua.pt>.

Visualization

To see the possible options of FALCON-EYE type
./FALCON-EYE
or
./FALCON-EYE -h
These will print the following options:
Usage: FALCON-EYE [OPTION]... [FILE]
Visualize FALCON-FILTER output.

  -h                       give this help,
  -F                       force mode (overwrites top file),
  -V                       display version number,
  -v                       verbose mode (more information),
  -w  <width>              square width (for each value),
  -s  <ispace>             square inter-space (between each value),
  -i  <indexs>             color index start,
  -r  <indexr>             color index rotations,
  -u  <hue>                color hue,
  -sl <lower>              similarity lower bound,
  -su <upper>              similarity upper bound,
  -dl <lower>              size lower bound,
  -du <upper>              size upper bound,
  -bg                      show only the best of group,
  -g  <color>              color gamma,
  -e  <size>               enlarge painted regions,
  -ss                      do NOT show global scale,
  -sn                      do NOT show names,
  -o  <FILE>               output image filename,

Mandatory arguments:

  [FILE]                   profile filename (from FALCON-FILTER),

Report issues to <{pratas,ap,pjf,jmr}@ua.pt>.

License

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