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.
- 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 also install numpy and scipy
pip3 install metagenomics-focus
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.
# these steps should install Numpy and Scipy
# clone focus
git clone git@github.com: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
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
The query can be one or more fasta or fastq files, or a directory containing those files. We filter for
files that end .fasta, .fastq, or .fna, so please ensure any file that you want processed has one
of those file extensions.
You can provide a mixture of input files or directories, and we will filter the files as appropriate.
For example:
focus -q fastq1.fastq -q fastq2.fastq -q directory/ -o outputwill process the two fastq files fastq1.fastq and fastq2.fastq as well as any fasta or fastq files in directory
and put the output in 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.
New genomes 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
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.