Snakemake workflow for metagenomic classification with Kraken2
☆67Jun 7, 2023Updated 2 years ago
Alternatives and similar repositories for kraken2_classification
Users that are interested in kraken2_classification are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Computational workflows for metagenomics tasks, by the Bhatt lab☆47Feb 6, 2023Updated 3 years ago
- KrakenTools provides individual scripts to analyze Kraken/Kraken2/Bracken/KrakenUniq output files☆371Aug 1, 2025Updated 7 months ago
- A simple nextflow pipeline for running kraken2 and bracken in a docker container☆20Oct 8, 2025Updated 5 months ago
- A GPU-accelerated method for ultrarapid pathogen identification from metagenomic sequences.☆29Jun 4, 2024Updated last year
- kASA - k-Mer Analysis of Sequences based on Amino acid-like encoding☆23Aug 23, 2023Updated 2 years ago
- The second version of the Kraken taxonomic sequence classification system☆879Mar 10, 2026Updated last week
- ganon2 classifies genomic sequences against large sets of references efficiently, with integrated download and update of databases (refse…☆104Mar 16, 2026Updated last week
- Accurate metagenomic profiling && Fast large-scale sequence/genome searching☆208Sep 22, 2023Updated 2 years ago
- ☆17Dec 5, 2017Updated 8 years ago
- A simple program to classify the lifestyle of phages.☆17May 22, 2023Updated 2 years ago
- Conversion software tool for producing both annotation and tree files for GraPhlAn☆11Feb 2, 2022Updated 4 years ago
- This repository houses the code to run SURPI+, a rapid computational pipeline for comprehensive identification of pathogens from clinical…☆42Nov 20, 2019Updated 6 years ago
- Bracken (Bayesian Reestimation of Abundance with KrakEN) is a highly accurate statistical method that computes the abundance of species i…☆339Mar 16, 2026Updated last week
- Pipeline for metabolic annotation of microbial genomes☆150Mar 20, 2025Updated last year
- Novelty-inclusive microbial (and now dsDNA phage) community profiling of shotgun metagenomes☆183Updated this week
- ShortBRED is a pipeline to take a set of protein sequences, reduce them to a set of unique identifying strings ("markers"), and then sear…☆31Jan 24, 2025Updated last year
- ☆17Jul 27, 2023Updated 2 years ago
- FlexTaxD (Flexible Taxonomy Databases) - Create, add, merge different taxonomy sources (QIIME, GTDB, NCBI and more) and create metagenomi…☆67Mar 15, 2026Updated last week
- Workflow to rapidly quantify taxa from all domains of life, directly from short-read human gut metagenomes☆71Dec 1, 2025Updated 3 months ago
- 🌈 Interactive analysis of metagenomics data☆445Sep 17, 2025Updated 6 months ago
- ☆13Aug 15, 2025Updated 7 months 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
- Identify and remove contaminants from metagenome-assembled genomes☆18Feb 16, 2024Updated 2 years ago
- A tool for removing redundant genomes from a set of assemblies☆79Sep 10, 2025Updated 6 months ago
- Variational autoencoder for metagenomic binning☆319Feb 23, 2026Updated last month
- R implementation of the LEfSe method☆64Nov 17, 2025Updated 4 months ago
- Python package for detection of chimerism and contamination in prokaryotic genomes.☆82Mar 12, 2026Updated last week
- 🐙 KrakenUniq: Metagenomics classifier with unique k-mer counting for more specific results☆244Jan 18, 2024Updated 2 years ago
- MEGARes and AmrPlusPlus - A comprehensive database of antimicrobial resistance genes and user-friendly pipeline for analysis of high-thro…☆26Nov 14, 2022Updated 3 years ago
- ☆12Jan 29, 2020Updated 6 years ago
- Portable WDL workflows for IDseq production pipelines☆32Jan 19, 2022Updated 4 years ago
- Fast, robust ANI and aligned fraction for (metagenomic) genomes and contigs.☆240Oct 12, 2025Updated 5 months ago
- ☆45Jun 27, 2023Updated 2 years ago
- Metagenomic classification of long-read sequencing data☆103Jan 22, 2026Updated 2 months ago
- An integrated pipeline for estimating strain-level genomic variation from metagenomic data☆132Oct 6, 2023Updated 2 years ago
- customizable pipeline to identify viral sequences from (meta)genomic data☆283Nov 28, 2024Updated last year
- Database of genomes integrated from the gut microbiome and other environments☆45Feb 3, 2023Updated 3 years ago
- Bioinformatics program inStrain☆182Mar 12, 2026Updated last week
- A repository for the lessons and notebooks used for Binder tutorials☆16Oct 24, 2020Updated 5 years ago