taxonkit
A command-line toolkit for efficient querying and manipulation of NCBI Taxonomy data, with support for custom taxonomies.
What is taxonkit?
TaxonKit is a command-line utility for fast and practical operations on NCBI Taxonomy data. It enables bioinformaticians and researchers to query lineages, filter taxa, compute lowest common ancestors, and manage taxonomic identifiers with high performance. The toolkit is essential for metagenomic analysis, taxonomic profiling, and database curation workflows.
Bioinformaticians and researchers who need to process NCBI taxonomic data in high-throughput pipelines, such as those working on metagenomic analysis, taxonomic profiling, or database curation.
Developers choose TaxonKit for its high performance, ease of use with statically compiled binaries and no dependencies, and versatility in handling custom taxonomies like GTDB and ICTV through NCBI-style taxdump creation.
Overview
A Practical and Efficient NCBI Taxonomy Toolkit, also supports creating NCBI-style taxdump files for custom taxonomies like GTDB/ICTV
Use Cases
Best For
- Retrieving complete taxonomic lineages for given TaxIds in metagenomic profiling workflows.
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