shenwei356 / taxonkit
A Practical and Efficient NCBI Taxonomy Toolkit, also supports creating NCBI-style taxdump files for custom taxonomies like GTDB/ICTV
☆401Updated last month
Alternatives and similar repositories for taxonkit:
Users that are interested in taxonkit are comparing it to the libraries listed below
- Rapid & standardized annotation of bacterial genomes, MAGs & plasmids☆486Updated 2 weeks ago
- NCBI Prokaryotic Genome Annotation Pipeline☆329Updated last week
- Resistance Gene Identifier (RGI). Software to predict resistomes from protein or nucleotide data, including metagenomics data, based on h…☆354Updated 2 weeks ago
- Eukaryotic Genome Annotation Pipeline☆337Updated this week
- NEW location of IQ-TREE software for efficient phylogenomic software by maximum likelihood http://www.iqtree.org☆271Updated last week
- Assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes☆360Updated 6 months ago
- MetaPhlAn is a computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data☆328Updated last week
- KrakenTools provides individual scripts to analyze Kraken/Kraken2/Bracken/KrakenUniq output files☆329Updated last year
- MetaWRAP - a flexible pipeline for genome-resolved metagenomic data analysis☆415Updated last year
- Fast genome-wide functional annotation through orthology assignment☆596Updated 10 months ago
- BRAKER is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET/EP/ETP and AUGUSTUS in novel eu…☆388Updated last month
- Rapid comparison and dereplication of genomes☆276Updated 2 months ago
- A tool for generating consensus long-read assemblies for bacterial genomes☆316Updated 9 months ago
- A genome visualization python package for comparative genomics☆312Updated 2 months ago
- Fast Whole-Genome Similarity (ANI) Estimation☆395Updated last year
- (Not Offical) BBMap short read aligner, and other bioinformatic tools.☆221Updated 4 years ago
- Bracken (Bayesian Reestimation of Abundance with KrakEN) is a highly accurate statistical method that computes the abundance of species i…☆303Updated 2 weeks ago
- MCScanX: Multiple Collinearity Scan toolkit X version. The most popular synteny analysis tool in the world!☆250Updated 2 months ago
- ATLAS - Three commands to start analyzing your metagenome data☆384Updated 2 months ago
- ☆235Updated 9 months ago
- A complete pipeline for metagenomic analysis☆399Updated last week
- quality filtering tool for long reads☆322Updated last year
- Pilon is an automated genome assembly improvement and variant detection tool☆353Updated 2 years ago
- HUMAnN is the next generation of HUMAnN 1.0 (HMP Unified Metabolic Analysis Network).☆186Updated 6 months ago
- Sequence correction provided by ONT Research☆440Updated 5 months ago
- bioBakery tools for meta'omic profiling☆272Updated 4 months ago
- Rapid large-scale prokaryote pan genome analysis☆337Updated 2 years ago
- Rapid haploid variant calling and core genome alignment☆498Updated 7 months ago
- Informed prediction and analysis of bacterial metabolic pathways and genome-scale networks☆174Updated last week
- A flexible pipeline for complete analysis of bacterial genomes☆445Updated this week