The second version of the Kraken taxonomic sequence classification system
☆875Feb 19, 2026Updated 2 weeks ago
Alternatives and similar repositories for kraken2
Users that are interested in kraken2 are comparing it to the libraries listed below
Sorting:
- Bracken (Bayesian Reestimation of Abundance with KrakEN) is a highly accurate statistical method that computes the abundance of species i…☆338Feb 26, 2025Updated last year
- KrakenTools provides individual scripts to analyze Kraken/Kraken2/Bracken/KrakenUniq output files☆367Aug 1, 2025Updated 7 months ago
- Interactively explore metagenomes and more from a web browser.☆493Dec 22, 2021Updated 4 years ago
- 🌈 Interactive analysis of metagenomics data☆442Sep 17, 2025Updated 5 months ago
- Ultra-fast and memory-efficient (meta-)genome assembler☆696Oct 28, 2025Updated 4 months ago
- SPAdes Genome Assembler☆912Feb 26, 2026Updated last week
- MetaPhlAn is a computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data☆394Dec 13, 2025Updated 2 months ago
- Classifier for metagenomic sequences☆271Jun 20, 2025Updated 8 months ago
- MetaWRAP - a flexible pipeline for genome-resolved metagenomic data analysis☆460Jul 28, 2023Updated 2 years ago
- hybrid assembly pipeline for bacterial genomes☆634Jul 25, 2024Updated last year
- An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)☆2,297Jan 22, 2026Updated last month
- Rapid prokaryotic genome annotation☆957Jan 6, 2026Updated 2 months ago
- 🐙 KrakenUniq: Metagenomics classifier with unique k-mer counting for more specific results☆244Jan 18, 2024Updated 2 years ago
- Fast taxonomic classification of metagenomic sequencing reads using a protein reference database☆301Apr 25, 2025Updated 10 months ago
- De novo assembler for single molecule sequencing reads using repeat graphs☆906May 2, 2025Updated 10 months ago
- GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.☆582Feb 21, 2026Updated 2 weeks ago
- Kraken taxonomic sequence classification system☆221Sep 27, 2021Updated 4 years ago
- Prodigal Gene Prediction Software☆525Jan 23, 2024Updated 2 years ago
- Accelerated BLAST compatible local sequence aligner.☆1,249Updated this week
- AMRFinderPlus - Identify AMR genes and point mutations, and virulence and stress resistance genes in assembled bacterial nucleotide and p…☆353Feb 27, 2026Updated last week
- Rapid & standardized annotation of bacterial genomes, MAGs & plasmids☆607Feb 18, 2026Updated 2 weeks ago
- Resistance Gene Identifier (RGI). Software to predict resistomes from protein or nucleotide data, including metagenomics data, based on h…☆402Jan 12, 2026Updated last month
- Genome assembly evaluation tool☆502Nov 14, 2024Updated last year
- Fast genome and metagenome distance estimation using MinHash☆435Sep 19, 2025Updated 5 months ago
- Assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes☆403Updated this week
- Fast genome-wide functional annotation through orthology assignment☆704Jun 18, 2025Updated 8 months ago
- Mass screening of contigs for antimicrobial and virulence genes☆481Jan 31, 2026Updated last month
- Rapid haploid variant calling and core genome alignment☆569Dec 12, 2025Updated 2 months ago
- adapter trimmer for Oxford Nanopore reads☆384May 8, 2024Updated last year
- A versatile pairwise aligner for genomic and spliced nucleotide sequences☆2,133Feb 13, 2026Updated 3 weeks ago
- a Bioinformatics Application for Navigating De novo Assembly Graphs Easily☆666Dec 3, 2022Updated 3 years ago
- quality filtering tool for long reads☆395Sep 17, 2025Updated 5 months ago
- Mummer alignment tool☆550Feb 4, 2025Updated last year
- Fast Whole-Genome Similarity (ANI) Estimation☆448Dec 16, 2025Updated 2 months ago
- HUMAnN is the next generation of HUMAnN 1.0 (HMP Unified Metabolic Analysis Network).☆235Jan 20, 2026Updated last month
- Recentrifuge: robust comparative analysis and contamination removal for metagenomics☆100Feb 10, 2026Updated 3 weeks ago
- customizable pipeline to identify viral sequences from (meta)genomic data☆282Nov 28, 2024Updated last year
- A Practical and Efficient NCBI Taxonomy Toolkit, also supports creating NCBI-style taxdump files for custom taxonomies like GTDB/ICTV☆459Feb 13, 2026Updated 3 weeks ago
- Sequence correction provided by ONT Research☆500Dec 8, 2025Updated 2 months ago