A Practical and Efficient NCBI Taxonomy Toolkit, also supports creating NCBI-style taxdump files for custom taxonomies like GTDB/ICTV
☆470Mar 20, 2026Updated 2 months ago
Alternatives and similar repositories for taxonkit
Users that are interested in taxonkit are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Accurate metagenomic profiling && Fast large-scale sequence/genome searching☆217Apr 24, 2026Updated last month
- A cross-platform and ultrafast toolkit for FASTA/Q file manipulation☆1,555May 22, 2026Updated last week
- Read alignment statistics for metagenomics☆397Apr 8, 2026Updated last month
- Rapid & standardized annotation of bacterial genomes, MAGs & plasmids☆643May 15, 2026Updated 2 weeks ago
- Fast Whole-Genome Similarity (ANI) Estimation☆461Dec 16, 2025Updated 5 months ago
- Wordpress hosting with auto-scaling - Free Trial Offer • AdFully Managed hosting for WordPress and WooCommerce businesses that need reliable, auto-scalable performance. Cloudways SafeUpdates now available.
- A versatile toolkit for k-mers with taxonomic information☆82Aug 28, 2025Updated 9 months ago
- Scripts to download genomes from the NCBI FTP servers☆1,077Apr 7, 2026Updated last month
- GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.☆599May 20, 2026Updated last week
- Fast, robust ANI and aligned fraction for (metagenomic) genomes and contigs.☆252May 13, 2026Updated 2 weeks ago
- Rapid comparison and dereplication of genomes☆341Nov 10, 2025Updated 6 months ago
- LexicMap: efficient sequence alignment against millions of prokaryotic genomes☆219Updated this week
- Fast genome-wide functional annotation through orthology assignment☆737May 22, 2026Updated last week
- KrakenTools provides individual scripts to analyze Kraken/Kraken2/Bracken/KrakenUniq output files☆374Aug 1, 2025Updated 9 months ago
- Gene cluster comparison figure generator☆641Dec 22, 2025Updated 5 months ago
- GPU virtual machines on DigitalOcean Gradient AI • AdGet to production fast with high-performance AMD and NVIDIA GPUs you can spin up in seconds. The definition of operational simplicity.
- A cross-platform, efficient and practical CSV/TSV toolkit in Golang☆1,159May 2, 2026Updated 3 weeks ago
- More scalable dereplication for metagenome assembled genomes☆81May 16, 2026Updated last week
- Mummer alignment tool☆560Feb 4, 2025Updated last year
- Rapid haploid variant calling and core genome alignment☆585Dec 12, 2025Updated 5 months ago
- Create a tree using Mash distances☆188Oct 24, 2023Updated 2 years ago
- Cython bindings and Python interface to Prodigal, an ORF finder for genomes and metagenomes. Now with SIMD!☆187Mar 17, 2026Updated 2 months ago
- Quickly search, compare, and analyze genomic and metagenomic data sets.☆542May 21, 2026Updated last week
- Assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes☆409Mar 2, 2026Updated 2 months ago
- A Python package for obtaining complete lineages and the lowest common ancestor (LCA) from a set of taxonomic identifiers☆59Mar 27, 2026Updated 2 months ago
- Deploy to Railway using AI coding agents - Free Credits Offer • AdUse Claude Code, Codex, OpenCode, and more. Autonomous software development now has the infrastructure to match with Railway.
- Align proteins to genomes with splicing and frameshift☆404Jan 5, 2026Updated 4 months ago
- Novelty-inclusive microbial (and now dsDNA phage) community profiling of shotgun metagenomes☆188May 18, 2026Updated last week
- Assessing the quality of metagenome-derived genome bins using machine learning☆263Mar 20, 2025Updated last year
- A grammar of graphics for comparative genomics☆762Feb 23, 2026Updated 3 months ago
- CAMISIM: Simulating metagenomes and microbial communities☆225May 20, 2026Updated last week
- geNomad: Identification of mobile genetic elements☆313Mar 29, 2026Updated 2 months ago
- Genome assembly evaluation tool☆510Nov 14, 2024Updated last year
- Python bindings for the TaxonKit library☆43Apr 6, 2026Updated last month
- ultrafast taxonomic profiling and genome querying for metagenomic samples by abundance-corrected minhash.☆304Feb 3, 2026Updated 3 months ago
- Deploy on Railway without the complexity - Free Credits Offer • AdConnect your repo and Railway handles the rest with instant previews. Quickly provision container image services, databases, and storage volumes.
- Mass screening of contigs for antimicrobial and virulence genes☆493Apr 3, 2026Updated last month
- SemiBin: metagenomics binning with self-supervised deep learning☆162Updated this week
- CAT/BAT/RAT: tools for taxonomic classification of contigs and metagenome-assembled genomes (MAGs) and for taxonomic profiling of metage…☆230Apr 1, 2026Updated last month
- Generic but comprehensive pipeline for prokaryotic genome annotation and interrogation with interactive reports and shiny app.☆107Jan 22, 2026Updated 4 months ago
- Build a partitioned pangenome graph from microbial genomes☆302Updated this week
- a python package for fast random access to sequences from plain and gzipped FASTA/Q files☆295Jan 16, 2026Updated 4 months ago
- Bracken (Bayesian Reestimation of Abundance with KrakEN) is a highly accurate statistical method that computes the abundance of species i…☆350Mar 16, 2026Updated 2 months ago