Python bindings for the TaxonKit library
☆43Feb 2, 2026Updated last month
Alternatives and similar repositories for pytaxonkit
Users that are interested in pytaxonkit are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- A Python package for obtaining, parsing and exploring biological taxonomies (GTDB, NCBI, Silva, Greengenes, OTT)☆48Feb 5, 2026Updated last month
- Mapping NCBI Genbank accession to GTDB accession☆14Feb 13, 2021Updated 5 years ago
- A Python package for obtaining complete lineages and the lowest common ancestor (LCA) from a set of taxonomic identifiers☆53Jan 23, 2026Updated 2 months ago
- Just another minhash implementation.☆12Mar 12, 2026Updated last week
- Robust individual and aggregate checksums for nucleotide sequences☆17Mar 3, 2026Updated 3 weeks ago
- Taxon Information Query - fast, offline querying of NCBI Taxonomy and related data☆60Feb 8, 2026Updated last month
- Finding prophage regions in bacterial genomes using brute force☆22Jan 20, 2023Updated 3 years ago
- PyO3 bindings and Python interface to sylph, an ultrafast method for containment ANI querying and taxonomic profiling.☆20Dec 12, 2024Updated last year
- Pipeline for metagenomic community analysis using DNA isolated from virus-like particles☆13Mar 21, 2020Updated 6 years ago
- a command line tool for viral proteomic tree generation, part of the ViPTree project: http://www.genome.jp/viptree☆35Sep 20, 2022Updated 3 years ago
- NCBI-style taxdump files for International Committee on Taxonomy of Viruses (ICTV)☆22May 3, 2025Updated 10 months ago
- Python library for identification and masking of low-complexity regions in nucleotide sequences☆10Jan 23, 2026Updated 2 months ago
- TAXnomic Profile Aggregation and STAndardisation☆42Nov 18, 2025Updated 4 months ago
- A Practical and Efficient NCBI Taxonomy Toolkit, also supports creating NCBI-style taxdump files for custom taxonomies like GTDB/ICTV☆464Updated this week
- 🐦 spideog - Command line utility for Kraken2 reports.☆11Nov 30, 2020Updated 5 years ago
- Fasten toolkit, for streaming operations on fastq files☆81Oct 24, 2025Updated 5 months ago
- Fast and accurate tool for calculating Average Nucleotide Identity (ANI) and clustering virus genomes and metagenomes☆106May 23, 2025Updated 10 months ago
- MetagenOmic read Re-Assigner and abundance quantifier☆20Jan 31, 2025Updated last year
- ☆10Dec 22, 2025Updated 3 months ago
- A tool in order to accurately remove primer sequences from NGS reads in an amplicon experiment☆20Nov 12, 2025Updated 4 months ago
- Real-time species-typing visualisation for nanopore data.☆13Apr 11, 2023Updated 2 years ago
- A versatile toolkit for k-mers with taxonomic information☆82Aug 28, 2025Updated 6 months ago
- A pipeline for high-quality bacterial genome construction using ONT sequencing☆38Sep 22, 2022Updated 3 years ago
- Better and faster Rust implementation of the FragGeneScan gene prediction model for short and error-prone reads.☆31Feb 3, 2026Updated last month
- Python package for detection of chimerism and contamination in prokaryotic genomes.☆82Mar 12, 2026Updated last week
- PyO3 bindings and Python interface to skani, a method for fast genomic identity calculation using sparse chaining.☆29Aug 20, 2025Updated 7 months ago
- A graph-inspired data structure for determining likely chains of sequences from breadcrumbs of evidence☆17Jun 29, 2021Updated 4 years ago
- ultrafast taxonomic profiling and genome querying for metagenomic samples by abundance-corrected minhash.☆298Feb 3, 2026Updated last month
- URMAP ultra-fast read mapper☆38Jun 15, 2020Updated 5 years ago
- TaxTriage is a Nextflow workflow designed to agnostically identify and classify microbial organisms within short- or long-read metagenomi…☆63Mar 18, 2026Updated last week
- annotation pipeline for microbial genomes and metagenomes☆18Feb 23, 2018Updated 8 years ago
- Development repo for pyani-plus (the next iteration of pyani)☆27Mar 16, 2026Updated last week
- deduplicate FASTA and FASTQ files☆23Feb 16, 2022Updated 4 years ago
- StrainEst - abundance estimation of strains☆20Jan 17, 2020Updated 6 years ago
- A post-processing tool to reclassify Kraken 2 output based on the confidence score and/or minimum minimizer hit groups.☆10Nov 10, 2025Updated 4 months ago
- A Nextflow pipeline for viral genomics (Influenza/RSV) supporting Illumina and Nanopore sequencing of clinical and wastewater samples.☆10Feb 27, 2026Updated 3 weeks ago
- WtP: Phage identification via nextflow and docker or singularity☆104Updated this week
- A database for signatures of public genomic sources☆18Jan 1, 2026Updated 2 months ago
- a python package for fast random access to sequences from plain and gzipped FASTA/Q files☆290Jan 16, 2026Updated 2 months ago