{"categories":[{"label":"Python Modules","url":"https://skillfed.io/packages/category/software-development-libraries-python-modules/19"},{"label":"Bio-Informatics","url":"https://skillfed.io/packages/category/scientific-engineering-bio-informatics"},{"label":"Medical Science Apps.","url":"https://skillfed.io/packages/category/scientific-engineering-medical-science-apps"}],"enrichment":{"capability":"Pysylph provides Python bindings to sylph, enabling fast ANI (Average Nucleotide Identity) querying and taxonomic profiling of metagenomic samples against genome databases.","skillfed_tags":["bioinformatics","genomics","metagenomics"],"use_cases":["Build and query genome sketch databases for rapid species identification in metagenomic samples","Perform taxonomic profiling of shotgun sequencing reads against reference genome collections","Integrate ANI containment queries into Python-based bioinformatics pipelines without CLI wrappers","Parallelize genome sketching or sample querying using ThreadPool for large-scale analyses","Load and query databases created by the standalone sylph binary within Python workflows"],"what_it_does":"Pysylph is a PyO3-based Python wrapper around sylph, a specialized bioinformatics tool for rapid ANI containment queries and metagenomic taxonomic profiling. It lets you sketch genome collections into searchable databases and query metagenomic samples against them to estimate species composition and sequence similarity. All computation happens in memory using Python objects you control, eliminating the need for temporary files or external binaries.\n\nThe package targets bioinformaticians and researchers working with shotgun metagenomic data. It uses a statistical model based on Poisson coverage to compute coverage-adjusted ANI rather than naive ANI, making it suitable for real-world sequencing data with uneven coverage. Pre-built wheels for x86-64 and Arm64 platforms reduce installation friction, though the package remains in alpha and explicitly warns of API instability between minor versions.","worth_installing":"Yes, if you are doing metagenomic profiling or ANI queries in Python and accept the alpha-stage API instability. The permissive MIT license, zero runtime dependencies, and pre-built wheels make installation straightforward. However, the 647-day gap since last release and dormant maintenance status mean you should verify that the current API meets your needs and be prepared to pin the version or fork if breaking changes occur in future releases."},"id":"pysylph","links":{"html":"https://skillfed.io/packages/pysylph","md":"https://skillfed.io/packages/pysylph.md","pypi":"https://pypi.org/project/pysylph/"},"maintenance":{"status":"dormant"},"meta":{"latest_release":"2024-11-05","license_spdx":null,"license_treatment":"permissive","name":"pysylph","python_support":"supports_current","summary":"PyO3 bindings and Python interface to sylph, an ultrafast method for containment ANI querying and taxonomic profiling."},"popularity":{"monthly_downloads":119037,"position":12092,"tier":"top_15000"},"security":{"n_vulnerabilities":0},"version":"0.1.2"}