Quality control tool on metagenomic and metatranscriptomic sequencing data, especially data from microbiome experiments.
☆150Dec 17, 2025Updated 6 months ago
Alternatives and similar repositories for kneaddata
Users that are interested in kneaddata are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- MetaPhlAn is a computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data☆411Jun 8, 2026Updated last week
- HUMAnN is the next generation of HUMAnN 1.0 (HMP Unified Metabolic Analysis Network).☆246Jun 11, 2026Updated last week
- MaAsLin2: Microbiome Multivariate Association with Linear Models☆155Feb 5, 2026Updated 4 months ago
- Assessing the quality of metagenome-derived genome bins using machine learning☆267Mar 20, 2025Updated last year
- Read alignment statistics for metagenomics☆399Jun 11, 2026Updated last week
- Serverless GPU API endpoints on Runpod - Get Bonus Credits • AdSkip the infrastructure headaches. Auto-scaling, pay-as-you-go, no-ops approach lets you focus on innovating your application.
- Assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes☆410Mar 2, 2026Updated 3 months ago
- Precise phylogenetic analysis of microbial isolates and genomes from metagenomes☆168Jun 10, 2026Updated last week
- Variational autoencoder for metagenomic binning☆328Apr 27, 2026Updated last month
- MetaWRAP - a flexible pipeline for genome-resolved metagenomic data analysis☆472Jul 28, 2023Updated 2 years ago
- R markdown documents copied from other folders on Dec 15th 2021☆14Nov 4, 2025Updated 7 months ago
- Workflow to rapidly quantify taxa from all domains of life, directly from short-read human gut metagenomes☆74Dec 1, 2025Updated 6 months ago
- Woltka: a versatile meta'omic data classifier☆80Sep 8, 2025Updated 9 months ago
- GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.☆607May 20, 2026Updated 3 weeks ago
- CAT/BAT/RAT: tools for taxonomic classification of contigs and metagenome-assembled genomes (MAGs) and for taxonomic profiling of metage…☆231Apr 1, 2026Updated 2 months ago
- Managed Database hosting by DigitalOcean • AdPostgreSQL, MySQL, MongoDB, Kafka, Valkey, and OpenSearch available. Automatically scale up storage and focus on building your apps.
- CLI tool to annotate genes with KOfam☆99Jun 6, 2023Updated 3 years ago
- Bioinformatics program inStrain☆188Mar 12, 2026Updated 3 months ago
- KrakenTools provides individual scripts to analyze Kraken/Kraken2/Bracken/KrakenUniq output files☆375Aug 1, 2025Updated 10 months ago
- The second version of the Kraken taxonomic sequence classification system☆912Jun 10, 2026Updated last week
- bioBakery workflows is a collection of workflows and tasks for executing common microbial community analyses using standardized, validate…☆137Apr 22, 2026Updated last month
- bioBakery tools for meta'omic profiling☆317Jun 3, 2025Updated last year
- motus - a tool for marker gene-based OTU (mOTU) profiling☆177Jun 11, 2026Updated last week
- Bracken (Bayesian Reestimation of Abundance with KrakEN) is a highly accurate statistical method that computes the abundance of species i…☆354Mar 16, 2026Updated 3 months ago
- CAMISIM: Simulating metagenomes and microbial communities☆226May 27, 2026Updated 3 weeks ago
- Managed hosting for WordPress and PHP on Cloudways • AdManaged hosting for WordPress, Magento, Laravel, or PHP apps, on multiple cloud providers. Deploy in minutes on Cloudways by DigitalOcean.
- Microbiome classification pipeline☆67May 13, 2025Updated last year
- Code, unit tests, and tutorials for running PICRUSt2☆389Nov 27, 2025Updated 6 months ago
- customizable pipeline to identify viral sequences from (meta)genomic data☆293Nov 28, 2024Updated last year
- ☆19Dec 16, 2024Updated last year
- geNomad: Identification of mobile genetic elements☆316Mar 29, 2026Updated 2 months ago
- ☆64Feb 27, 2024Updated 2 years ago
- 🚦🧬 Binning Metagenomic Contigs via Composition, Coverage and Assembly Graphs☆69Updated this week
- Distilled and Refined Annotation of Metabolism: A tool for the annotation and curation of function for microbial and viral genomes☆334Jun 3, 2026Updated 2 weeks ago
- Rapid & standardized annotation of bacterial genomes, MAGs & plasmids☆652May 15, 2026Updated last month
- Managed Database hosting by DigitalOcean • AdPostgreSQL, MySQL, MongoDB, Kafka, Valkey, and OpenSearch available. Automatically scale up storage and focus on building your apps.
- DAS Tool☆174May 2, 2024Updated 2 years ago
- Ultra-fast and memory-efficient (meta-)genome assembler☆719Oct 28, 2025Updated 7 months ago
- ultrafast taxonomic profiling and genome querying for metagenomic samples by abundance-corrected minhash.☆311Feb 3, 2026Updated 4 months ago
- SPAdes Genome Assembler☆942Jun 11, 2026Updated last week
- SemiBin: metagenomics binning with self-supervised deep learning☆164Jun 7, 2026Updated last week
- DeepMicrobes: taxonomic classification for metagenomics with deep learning☆106Sep 17, 2022Updated 3 years ago
- Improvement of metagenome-assembled genomes☆58Mar 17, 2020Updated 6 years ago