FOCUS: An Agile Profiler for Metagenomic Data

• Installation
• Usage
• Output
• Docker
• Changelog
• Citing

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Binning vs Profiling

FOCUS is a profiling tool — it estimates the relative abundance of organisms in a metagenome without assembling or binning reads. See this blog post for the distinction.

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Installation

Dependencies

Dependency	Version
Python	≥ 3.8
Jellyfish	2.x
NumPy	≥ 1.12.1
SciPy	≥ 0.19.0
Click	≥ 8.0

Bioconda (recommended)

conda install -c bioconda -c conda-forge focus

This installs FOCUS and Jellyfish automatically.

From source

git clone https://github.com/your-org/focus.git
cd focus

# extract the database (one-time)
cd focus_app && unzip db.zip && cd ..

# install with pip
pip install -e .

# or with uv (developer tool — not required for end users)
uv pip install -e .

Note: uv is a fast developer tool for managing Python environments. It is not a runtime dependency and is not required to install or use FOCUS. The package installs with standard pip or conda.

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Usage

focus [OPTIONS]

  FOCUS: An Agile Profiler for Metagenomic Data.

  Example: focus -q samples/ -o results/

Options:
  -v, --version                   Show version and exit.
  -q, --query TEXT                FAST(A/Q) file or directory (repeatable).  [required]
  -o, --output_directory TEXT     Directory for output CSV files.  [required]
  -k, --kmer_size [6|7]           K-mer size.  [default: 6]
  -b, --alternate_directory TEXT  Alternate directory containing the db/ folder.
  -p, --output_prefix TEXT        Prefix for output files.  [default: output]
  -t, --threads TEXT              Jellyfish thread count.  [default: 4]
  --list_output                   Return results as a list of lists.
  -l, --log TEXT                  Log file path (default: STDOUT).
  -h, --help                      Show this message and exit.

Examples

# single file
focus -q sample.fastq -o results/

# multiple files
focus -q sample1.fasta -q sample2.fastq -o results/

# directory of files, k-mer size 7, 8 threads
focus -q samples/ -o results/ -k 7 -t 8

# log to file
focus -q samples/ -o results/ -l run.log

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Output

One CSV per taxonomic level plus an all-levels file:

File	Contents
output_All_levels.csv	All 8 taxonomy columns + abundance per sample
output_Kingdom_tabular.csv	Kingdom-level aggregated abundances
…	Class, Order, Family, Genus, Species
output_Strain_tabular.csv	Strain-level abundances

Abundances are expressed as percentages (0–100). The all-levels file is compatible with STAMP.

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Docker

See Docker/README.md for build and Singularity instructions.

docker build -t focus .
docker run --rm \
  -v $(pwd)/samples:/data/samples \
  -v $(pwd)/results:/data/results \
  focus -q /data/samples -o /data/results

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Development

# install with dev dependencies (pip)
pip install -e ".[dev]"

# or with uv (faster)
uv pip install -e ".[dev]"

# run tests
pytest

# run tests with coverage
pytest --cov=focus_app --cov-report=term-missing

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Changelog

See CHANGELOG.

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Citing

If you use FOCUS, please cite:

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.