Pyskani

PyO3 bindings and Python interface to skani, a method for fast fast genomic identity calculation using sparse chaining.

Overview

skani is a method developed by Jim Shaw and Yun William Yu for fast and robust metagenomic sequence comparison through sparse chaining. It improves on FastANI by being more accurate and much faster, while requiring less memory.

pyskani is a Python module, implemented using the PyO3 framework, that provides bindings to skani. It directly links to the skani code, which has the following advantages over CLI wrappers:

• pre-built wheels: pyskani is distributed on PyPI and features pre-built wheels for common platforms, including x86-64 and Arm64 UNIX.

• single dependency: If your software or your analysis pipeline is distributed as a Python package, you can add pyskani as a dependency to your project, and stop worrying about the skani binary being present on the end-user machine.

• sans I/O: Everything happens in memory, in Python objects you control, making it easier to pass your sequences to skani without having to write them to a temporary file.

Setup

Pyskani is available for all modern Python versions supported by PyO3 (3.8+).

Run pip install pyskani in a shell to download the latest release and all its dependencies from PyPi, or have a look at the Installation page to find other ways to install pyskani.

Library

• User Guide
  • Installation
  • Contribution Guide
  • Changelog
  • Copyright Notice
• API Reference

Related Projects

The following Python libraries may be of interest for bioinformaticians.

PyHMMER

Profile Hidden Markov Models (with HMMER).

https://pyhmmer.readthedocs.io

Pyrodigal

Prokaryotic Gene Finding (with Prodigal).

https://pyrodigal.readthedocs.io

Pyrodigal-gv

Pyrodigal for Giant Viruses.

https://pypi.org/project/pyrodigal-gv/

PyFAMSA

Multiple Sequence Alignment (with FAMSA).

https://pyfamsa.readthedocs.io

PytrimAl

Alignment Trimming (with trimAl).

https://pytrimal.readthedocs.io

LightMotif

Platform-accelerated motif scoring.

https://lightmotif.readthedocs.io

Diced

CRISPR Detection (with MinCED).

https://diced.readthedocs.io

Scoring Matrices

Scoring matrices for Cython.

https://scoring-matrices.readthedocs.io

Pyskani

Average Nucleotide Identity (with skani).

https://pyskani.readthedocs.io

PySylph

ANI containment and taxonomic profiling (with sylph).

https://pysylph.readthedocs.io

PyFastANI

Average Nucleotide Identity (with FastANI).

https://pyfastani.readthedocs.io

PyJess

Geometric Template Matching (with Jess).

https://pyjess.readthedocs.io

PyTantan

Tandem Repeat Masking (with Tantan).

https://pytantan.readthedocs.io

PyOpal

Query/Database Aligner (with Opal).

https://pyopal.readthedocs.io

PySWRD

Database Heuristic Filtering (with SWORD).

https://pyswrd.readthedocs.io

Mini3di

Protein structure to 3di in pure Python.

https://pypi.org/project/mini3di/

peptides.py

Peptide descriptors for Python.

https://peptides.readthedocs.io

Pronto

Open Biomedical Ontologies for Python.

https://pronto.readthedocs.io

NAFcodec

Nucleotide Archival Format for Python (and Rust).

https://pypi.org/project/nafcodec/

gb-io.py

Fast GenBank parser for Python (with gb-io).

https://gb-io.readthedocs.io

PyOrthoANI

OrthoAni re-implementation in Python.

https://pypi.org/project/pyorthoani/

PyCoMSA

Multiple Sequence Alignment compression (with CoMSA).

https://pycomsa.readthedocs.io

PyARAGORN

tRNA, tmRNA and mtRNA gene prediction (with ARAGORN).

https://pyaragorn.readthedocs.io

License

This library is provided under the MIT License.

The skani code was written by Jim Shaw and is distributed under the terms of the MIT License as well. Source distributions of pyskani may vendors additional sources under their own terms using the cargo vendor command.

This project is in no way not affiliated, sponsored, or otherwise endorsed by the original skani authors. It was developed by Martin Larralde during his PhD project at the European Molecular Biology Laboratory in the Zeller team.