shenwei356 / gtdb-taxdumpView external linksLinks
GTDB taxonomy taxdump files with trackable TaxIds
☆57Apr 29, 2025Updated 9 months ago
Alternatives and similar repositories for gtdb-taxdump
Users that are interested in gtdb-taxdump are comparing it to the libraries listed below
Sorting:
- Convert GTDB taxonomy to NCBI taxdump format☆74Aug 24, 2023Updated 2 years ago
- Scalable creating/updating of metagenome profiling databases☆62Jun 25, 2025Updated 7 months ago
- Ley Lab MetaGenome Profiler DataBase generator☆49Nov 9, 2022Updated 3 years ago
- Accurate metagenomic profiling && Fast large-scale sequence/genome searching☆205Sep 22, 2023Updated 2 years ago
- FlexTaxD (Flexible Taxonomy Databases) - Create, add, merge different taxonomy sources (QIIME, GTDB, NCBI and more) and create metagenomi…☆67Mar 12, 2025Updated 11 months ago
- ☆15Jan 22, 2026Updated 3 weeks ago
- a comparative genome browser for bacteriophages☆20Jan 17, 2025Updated last year
- Meteor is a plateform for quantitative metagenomics profiling of complex ecosystems. Meteor relies on genes catalogue to perform species-…☆35Dec 19, 2025Updated last month
- taxonomic classifier based on the kraken2 algorithms and more☆46Dec 12, 2025Updated 2 months ago
- Metabuli: specific and sensitive metagenomic classification via joint analysis of DNA and amino acid.☆166Jan 2, 2026Updated last month
- Fast, robust ANI and aligned fraction for (metagenomic) genomes and contigs.☆235Oct 12, 2025Updated 4 months ago
- LexicMap: efficient sequence alignment against millions of prokaryotic genomes☆209Updated this week
- MetaMDBG: a lightweight assembler for long and accurate metagenomics reads.☆199Feb 2, 2026Updated 2 weeks ago
- Snakemake pipeline for downstream analysis of metagenome-assembled genomes (MAGs) (pronounced mag-pie)☆61Apr 1, 2023Updated 2 years ago
- A Practical and Efficient NCBI Taxonomy Toolkit, also supports creating NCBI-style taxdump files for custom taxonomies like GTDB/ICTV☆457Updated this week
- CAT/BAT/RAT: tools for taxonomic classification of contigs and metagenome-assembled genomes (MAGs) and for taxonomic profiling of metage…☆224Jan 20, 2026Updated 3 weeks ago
- Map query sequences to the assemblies of all pre-June 2023 bacteria (https://ftp.ebi.ac.uk/pub/databases/AllTheBacteria/Releases/0.2/) on…☆12May 22, 2024Updated last year
- Python package for detection of chimerism and contamination in prokaryotic genomes.☆79Nov 23, 2023Updated 2 years ago
- A variable-selection oriented LASSO bagging algorithm for biomarker development in omic-based translational research☆19Jul 7, 2023Updated 2 years ago
- A Python package for obtaining, parsing and exploring biological taxonomies (GTDB, NCBI, Silva, Greengenes, OTT)☆47Feb 5, 2026Updated last week
- GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.☆574Feb 9, 2026Updated last week
- Predicting plasmid contigs from assemblies using single copy marker genes, plasmid genes, kmers - Developed by Linda van der Graaf☆50Apr 16, 2024Updated last year
- A curated database of completed assemblies with taxonomy IDs☆48Updated this week
- Growth Rate Index (GRiD) measures bacterial growth rate from reference genomes (including draft quality genomes) and metagenomic bins at …☆32May 22, 2020Updated 5 years ago
- A tool for generating consensus long-read assemblies for bacterial genomes☆339Sep 11, 2025Updated 5 months ago
- Cython bindings and Python interface to Prodigal, an ORF finder for genomes and metagenomes. Now with SIMD!☆176Jan 7, 2026Updated last month
- R markdown documents copied from other folders on Dec 15th 2021☆14Nov 4, 2025Updated 3 months ago
- A tool easily taken advantage of for in silico serogrouping of Pseudomonas aeruginosa isolates☆13Aug 26, 2024Updated last year
- Remove contaminated contigs from genomes using k-mers and taxonomies.☆59Nov 3, 2023Updated 2 years ago
- StrainXpress is a de novo assembly method which base on overlap-layout-consensus (OLC) paradigm and can fast and accurately assemble high…☆13Mar 7, 2024Updated last year
- ultrafast taxonomic profiling and genome querying for metagenomic samples by abundance-corrected minhash.☆290Feb 3, 2026Updated last week
- From annotated genomes to metabolic screening in large scale microbiotas☆68Jan 16, 2026Updated last month
- Precise host read removal☆115Sep 4, 2025Updated 5 months ago
- SemiBin: metagenomics binning with self-supervised deep learning☆154Jan 23, 2026Updated 3 weeks ago
- De Bruijn graph representation in low memory☆35Jul 6, 2024Updated last year
- Extract subsets of ONT (Nanopore) reads based on time☆23Sep 12, 2024Updated last year
- MDMcleaner the assessment, classification and refinement tool for microbial dark matter SAGs and MAGs☆23Mar 19, 2023Updated 2 years ago
- MAGScoT - a MAG scoring and refinement tool☆43Oct 10, 2024Updated last year
- Assign taxonomic ranks based on evolutionary divergence.☆23Mar 28, 2022Updated 3 years ago