DaehwanKimLab / centrifugeView external linksLinks
Classifier for metagenomic sequences
☆270Jun 20, 2025Updated 7 months ago
Alternatives and similar repositories for centrifuge
Users that are interested in centrifuge are comparing it to the libraries listed below
Sorting:
- 🌈 Interactive analysis of metagenomics data☆442Sep 17, 2025Updated 4 months ago
- The second version of the Kraken taxonomic sequence classification system☆868Jan 30, 2026Updated 2 weeks ago
- Fast genome and metagenome distance estimation using MinHash☆434Sep 19, 2025Updated 4 months ago
- 🐙 KrakenUniq: Metagenomics classifier with unique k-mer counting for more specific results☆243Jan 18, 2024Updated 2 years ago
- Fast taxonomic classification of metagenomic sequencing reads using a protein reference database☆298Apr 25, 2025Updated 9 months ago
- GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.☆574Updated this week
- Assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes☆401Jun 12, 2025Updated 8 months ago
- Bracken (Bayesian Reestimation of Abundance with KrakEN) is a highly accurate statistical method that computes the abundance of species i…☆336Feb 26, 2025Updated 11 months ago
- DAS Tool☆169May 2, 2024Updated last year
- De novo assembler for single molecule sequencing reads using repeat graphs☆903May 2, 2025Updated 9 months ago
- hybrid assembly pipeline for bacterial genomes☆632Jul 25, 2024Updated last year
- Mummer alignment tool☆548Feb 4, 2025Updated last year
- Ultra-fast and memory-efficient (meta-)genome assembler☆693Oct 28, 2025Updated 3 months ago
- Kraken taxonomic sequence classification system☆221Sep 27, 2021Updated 4 years ago
- KrakenTools provides individual scripts to analyze Kraken/Kraken2/Bracken/KrakenUniq output files☆366Aug 1, 2025Updated 6 months ago
- quality filtering tool for long reads☆389Sep 17, 2025Updated 4 months ago
- adapter trimmer for Oxford Nanopore reads☆380May 8, 2024Updated last year
- Rapid prokaryotic genome annotation☆955Jan 6, 2026Updated last month
- Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads. http://genome.cshlp.org/content/early/2017/01/18/gr…☆296May 9, 2024Updated last year
- Recentrifuge: robust comparative analysis and contamination removal for metagenomics☆99Jan 4, 2026Updated last month
- A complete pipeline for metagenomic analysis☆440Jan 21, 2026Updated 3 weeks ago
- k-SLAM ultra fast alignment and taxonomic classification of metagenomic datasets☆23Nov 18, 2018Updated 7 years ago
- Classifier for metagenomic sequences☆30Nov 12, 2018Updated 7 years ago
- Prodigal Gene Prediction Software☆524Jan 23, 2024Updated 2 years ago
- A tool to circularize genome assemblies☆252Apr 6, 2024Updated last year
- Ultrafast de novo assembly for long noisy reads (though having no consensus step)☆352Jul 19, 2025Updated 6 months ago
- Read alignment statistics for metagenomics☆387Jan 16, 2026Updated 3 weeks ago
- Rapid haploid variant calling and core genome alignment☆565Dec 12, 2025Updated 2 months ago
- a Bioinformatics Application for Navigating De novo Assembly Graphs Easily☆666Dec 3, 2022Updated 3 years ago
- Metagenomic profiling and phylogenetic distances via common kmers☆42Jul 12, 2021Updated 4 years ago
- Variational autoencoder for metagenomic binning☆317Feb 2, 2026Updated last week
- A robust, extensible metagenomics pipeline☆174Updated this week
- ☆84Sep 13, 2023Updated 2 years ago
- Interactively explore metagenomes and more from a web browser.☆493Dec 22, 2021Updated 4 years ago
- BItsliced Genomic Signature Index - Efficient indexing and search in very large collections of WGS data☆124Aug 24, 2023Updated 2 years ago
- MetaPhlAn is a computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data☆391Dec 13, 2025Updated 2 months ago
- Assessing the quality of metagenome-derived genome bins using machine learning☆248Mar 20, 2025Updated 10 months ago
- De novo Extraction of Strains from MetAgeNomes☆72Jun 17, 2020Updated 5 years ago
- An updated pipeline for pangenome investigation☆341Jan 15, 2026Updated 3 weeks ago