transform patterns

Pheniqs is a flexible generic barcode classifier for high-throughput next-gen sequencing that caters to a wide variety of experimental designs and has been designed for efficient data processing. Features include:

Citing Pheniqs: Pheniqs 2.0: accurate, high-performance Bayesian decoding and confidence estimation for combinatorial barcode indexing on BMC Bioinformatics.

Please check out the intro talk given by Lior Galanti on April 29, 2021 for the NYU CGSB core lab.

Powerful and intuitive syntax

Noise and quality aware probabilistic classifier

Robust engineering

Easy to install or build

Easy to use

On this website, you will find everything you need to get started with Pheniqs: Installation and configuration, classifying reads, vignettes that will walk you through processing popular experimental designs, and information about how to leverage standardized SAM auxiliary tags to improve the reproducibility of your published data.

Pheniqs runs on all modern POSIX systems and provides an easy to learn command line interface with autocomplete and an extensible reusable configuration syntax. Pheniqs is an ideal utility to pre- and post-process sequence reads for other bioinformatics tools, and it may also be used simply to rapidly and efficiently interconvert a variety of standard sequence file formats without invoking any of its barcode processing features.

For more advanced users and sequencing core managers, we provide detailed build instructions and a custom package manager to easily build portable, statically linked, Pheniqs binaries for deployment on computing clusters. Developers can find code examples and API documention that enable them to expand Pheniqs with new classification algorithms and take advantage of the optimized multithreaded pipeline.

Installing Pheniqs

You can install pheniqs using the conda package manager on Linux

conda install -c bioconda -c conda-forge pheniqs

You can build the latest Pheniqs binary with this one line. Just paste it into a Linux or macOS terminal.

bash -c "$(curl -fsSL"