How to install TaxonKit on Ubuntu?

Download the static binary from the GitHub releases page, uncompress it with 'tar -zxvf', and copy it to a directory in your PATH, such as /usr/local/bin. Alternatively, use conda with 'conda install -c bioconda taxonkit' for a simpler install.

TaxonKit vs ETE3: which is better for taxonomy?

TaxonKit is faster for batch processing of NCBI taxonomy data, as shown in benchmarks, while ETE3 offers more features for phylogenetic tree visualization and interactive analysis. Choose TaxonKit for speed in pipelines, ETE3 for exploratory work.

How to update NCBI taxonomy data in TaxonKit?

Re-download the taxdump.tar.gz file from NCBI, extract it, and copy the updated names.dmp and nodes.dmp files to $HOME/.taxonkit, overriding the old ones. No tool reinstallation is needed.

Can TaxonKit handle GTDB taxonomy?

Yes, using the 'create-taxdump' subcommand, you can generate NCBI-style taxdump files for GTDB, but you need to provide GTDB taxonomy data in the required format. Pre-built files are available via related projects.

How to use TaxonKit in a bioinformatics pipeline?

TaxonKit supports STDIN and gzipped files, making it pipe-friendly. For example, chain commands like 'cat input.txt | taxonkit lineage | taxonkit reformat' to process TaxIds efficiently, with examples in the usage docs.

Is there a Python API for TaxonKit?

Yes, but it's a separate project called pytaxonkit, which provides Python bindings. TaxonKit itself is command-line only, so for direct Python integration, you'll need to use subprocess calls or the bindings.

Open-Awesome

taxonkit

MITGov0.20.0

A command-line toolkit for efficient querying and manipulation of NCBI Taxonomy data, with support for custom taxonomies.

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475 stars30 forks0 contributors

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.

Target Audience

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.

Value Proposition

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.
Filtering TaxIds based on a specified taxonomic rank range, such as at or below genus level.
Computing the lowest common ancestor (LCA) for sets of TaxIds in phylogenetic analysis.
Converting metagenomic profile tables to CAMI format and filtering taxa.
Creating NCBI-style taxdump files for custom taxonomies like GTDB and ICTV.
Tracking changes to TaxIds across NCBI taxonomy updates for data consistency.

Not Ideal For

Projects requiring real-time taxonomic queries via a web API or database interface
Workflows that rely heavily on graphical user interfaces for interactive data exploration
Teams using non-NCBI taxonomies without the resources to create custom taxdump files

Pros & Cons

Pros

Lightning-Fast Performance

Benchmarks in the README show TaxonKit processes lineage queries in seconds, outperforming alternatives like ETE3 and taxopy, making it ideal for high-throughput pipelines.

Dependency-Free Deployment

Statically compiled binaries for multiple platforms require no external dependencies, ensuring easy installation and portability, as emphasized in the features section.

Versatile Taxonomic Operations

Offers a comprehensive suite of subcommands, from lineage reformatting to LCA computation and custom taxdump creation, with detailed usage examples provided online.

Excellent Documentation

Includes extensive usage pages, tutorials, and even Chinese documentation, helping users quickly learn and apply the tool in various scenarios.

Cons

Manual Data Management

Users must manually download and configure NCBI taxdump files in a specific directory ($HOME/.taxonkit), adding setup overhead compared to tools with automated database handling.

Command-Line Only

Lacks a graphical user interface or built-in web API, limiting accessibility for users who prefer interactive or programmatic access without shell scripting.

Custom Taxonomy Complexity

While it supports custom taxonomies like GTDB, creating NCBI-style taxdump files requires additional data preparation steps, which can be non-trivial for novices.

Frequently Asked Questions

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