FOCUS: An Agile Profiler for Metagenomic Data

• Installation
  • dependencies
  • pip3
  • bioconda
  • git
• Usage
• Add Genomes to Database
• Output
• Citing

Binning vs Profiling

This blog post talks the difference between binning and profiling in case you are interested to learn about it, so you can learn if FOCUS is right for you - FOCUS is a profiling tool.

Installation

Dependencies

• Python 3.6
• Setuptools 36.0.1
• Jellyfish >= 2.2.6. if using macOS, use bioconda
• Numpy 1.12.1
• SciPy 0.19.0
• unzip/curl

pip3

# pip3 also install numpy and scipy
pip3 install metagenomics-focus

Bioconda

You can now easily install FOCUS using conda via the Bioconda channel. It is as easy as:

# bioconda should handle all the dependencies
conda create -n focus -c bioconda focus
source activate focus

This will create a conda environment called focus (as specified by the -n argument), and install FOCUS along with all its dependencies. The second line activates the newly created focus conda environment.

Git

# these steps should install Numpy and Scipy

# clone focus
git clone [email protected]:metageni/FOCUS.git

# unzip database and move it to folder
unzip FOCUS/focus_app/db.zip && mv db FOCUS/focus_app/

# install focus
cd FOCUS && python setup.py install

Usage

focus [-h] [-v] -q QUERY -o OUTPUT_DIRECTORY [-k KMER_SIZE]
         [-b ALTERNATE_DIRECTORY] [-p OUTPUT_PREFIX] [-t THREADS]
         [--list_output] [-l LOG]

FOCUS: An Agile Profiler for Metagenomic Data

optional arguments:
  -h, --help            show this help message and exit
  -v, --version         show program's version number and exit
  -q QUERY, --query QUERY
                        Path to directory with FAST(A/Q) files
  -o OUTPUT_DIRECTORY, --output_directory OUTPUT_DIRECTORY
                        Path to output files
  -k KMER_SIZE, --kmer_size KMER_SIZE
                        K-mer size (6 or 7) (Default: 6)
  -b ALTERNATE_DIRECTORY, --alternate_directory ALTERNATE_DIRECTORY
                        Alternate directory for your databases
  -p OUTPUT_PREFIX, --output_prefix OUTPUT_PREFIX
                        Output prefix (Default: output)
  -t THREADS, --threads THREADS
                        Number Threads used in the k-mer counting (Default: 4)
  --list_output         Output results as a list
  -l LOG, --log LOG     Path to log file (Default: STDOUT).

example > focus -q samples_directory

Database

New genoems can be added into the database by using command focus_database_utils.

It only requires a (-g) a tabular file (\t) as input with a genome per row where the columns are composed by the metadata of the genome on Kingdom, Phylum, Class, Order, Family, Genus, Species, Strain, and path to FASTA file or the genome file.

usage: focus_database_utils [-h] [-v] -g GENOMES [-t THREADS] [-l LOG]

FOCUS Database Utils

optional arguments:
  -h, --help            show this help message and exit
  -v, --version         show program's version number and exit
  -g GENOMES, --genomes GENOMES
                        Path to directory with FAST(A/Q) files
  -t THREADS, --threads THREADS
                        Number Threads used in the k-mer counting (Default: 4)
  -l LOG, --log LOG     Path to log file (Default: STDOUT).

example > focus_database_utils -m GENOMES_TABULAR_FILE

Output

FOCUS generates a tabular output per taxonomic level (Kingdom, Phylum, Class, Order, Family, Genus, Species, and Strain) and one with all levels which can be used as STAMP's input for statistical analysis.

Citing

FOCUS was written by Genivaldo G. Z. Silva. Feel free to contact me

If you use FOCUS, please cite it:

Silva, G. G. Z., D. A. Cuevas, B. E. Dutilh, and R. A. Edwards, 2014:
FOCUS: An alignment-free model to identify organisms in metagenomes
using non-negative least squares. PeerJ.