Create BIOM-format tables (http://biom-format.org) from Kraken output (http://ccb.jhu.edu/software/kraken/, https://github.com/DerrickWood/kraken).
☆59Feb 7, 2026Updated 2 months ago
Alternatives and similar repositories for kraken-biom
Users that are interested in kraken-biom are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Bracken (Bayesian Reestimation of Abundance with KrakEN) is a highly accurate statistical method that computes the abundance of species i…☆343Mar 16, 2026Updated last month
- ☆57Apr 8, 2026Updated last week
- KrakenTools provides individual scripts to analyze Kraken/Kraken2/Bracken/KrakenUniq output files☆372Aug 1, 2025Updated 8 months ago
- Simple statistical identification and removal of contaminants in marker-gene and metagenomics sequencing data☆170Sep 4, 2025Updated 7 months ago
- Microbiome classification pipeline☆67May 13, 2025Updated 11 months ago
- Wordpress hosting with auto-scaling - Free Trial • AdFully Managed hosting for WordPress and WooCommerce businesses that need reliable, auto-scalable performance. Cloudways SafeUpdates now available.
- MaAsLin2: Microbiome Multivariate Association with Linear Models☆153Feb 5, 2026Updated 2 months ago
- ALDEx_bioc is the working directory for updating bioconductor☆31Mar 27, 2026Updated 3 weeks ago
- 🌈 Interactive analysis of metagenomics data☆447Sep 17, 2025Updated 7 months ago
- Conversion software tool for producing both annotation and tree files for GraPhlAn☆11Feb 2, 2022Updated 4 years ago
- Kraken output generates a report for each datasets, this script takes these individual output and combines it to one file, where each col…☆23Jul 26, 2024Updated last year
- Creates a simple OTU table from Kraken2 report.☆13Oct 15, 2024Updated last year
- Bacterial GWAS analysis☆47Apr 7, 2026Updated last week
- A pipeline for the identification of fungi in public metagenomics datasets☆17Nov 23, 2020Updated 5 years ago
- genome_updater is a bash script that downloads and updates (non-redundant) snapshots of the NCBI Genomes repository (RefSeq/GenBank) with…☆168Updated this week
- Deploy open-source AI quickly and easily - Bonus Offer • AdRunpod Hub is built for open source. One-click deployment and autoscaling endpoints without provisioning your own infrastructure.
- power estimation for microbiome studies analyzed with pairwise distances and PERMANOVA☆39Nov 24, 2015Updated 10 years ago
- in silico plasmid extraction☆13Sep 18, 2017Updated 8 years ago
- An R package for analysis of microbiome relative abundance data using zero inflated beta GAMLSS and meta-analysis across microbiome studi…☆34Nov 12, 2020Updated 5 years ago
- DAS Tool☆171May 2, 2024Updated last year
- Repository of the integrated mouse gut metagenomic catalog☆20Mar 14, 2022Updated 4 years ago
- The second version of the Kraken taxonomic sequence classification system☆890Apr 1, 2026Updated 2 weeks ago
- Hclust2 is a handy tool for plotting heat-maps with several useful options to produce high quality figures that can be used in publicatio…☆13Jan 14, 2023Updated 3 years ago
- shotgun pipeline☆12Apr 3, 2019Updated 7 years ago
- This is a deep learning method for identification of viral contigs with short length from metagenomic data.☆10Dec 20, 2021Updated 4 years ago
- 1-Click AI Models by DigitalOcean Gradient • AdDeploy popular AI models on DigitalOcean Gradient GPU virtual machines with just a single click. Zero configuration with optimized deployments.
- Strain resolver for metagenomics☆80Aug 2, 2024Updated last year
- iMAP v1.0 (Pre-release): Integrated Microbiome Analysis Pipeline☆13Feb 10, 2026Updated 2 months ago
- METAgenomic LONgitudinal Differential Abundance method☆16Dec 17, 2019Updated 6 years ago
- A containerized bioinformatics pipeline for viral metagenomic data analysis☆37Apr 9, 2026Updated last week
- Variational autoencoder for metagenomic binning☆320Feb 23, 2026Updated last month
- Snakemake pipeline for downstream analysis of metagenome-assembled genomes (MAGs) (pronounced mag-pie)☆62Apr 1, 2023Updated 3 years ago
- Taxonomic classifier for sequencing reads (bulk and single-cell data, short and long read) using FM-index with run-block compressed BWT.☆88Apr 2, 2026Updated 2 weeks ago
- Pawsey workshop: containers for bioinformatics☆21Dec 3, 2018Updated 7 years ago
- Ultra-rapid detection of viral variants directly from sequencing data☆39Feb 17, 2026Updated 2 months ago
- AI Agents on DigitalOcean Gradient AI Platform • AdBuild production-ready AI agents using customizable tools or access multiple LLMs through a single endpoint. Create custom knowledge bases or connect external data.
- Bioinformatics pipeline for recovery and analysis of metagenome-assembled genomes☆54Oct 24, 2025Updated 5 months ago
- Functional Mapping and Analysis Pipeline for metagenomics and metatranscriptomics studies☆26Feb 28, 2023Updated 3 years ago
- FishTaco (Functional Shifts Taxonomic Contributors) is a metagenomic computational framework that aims to identify the driver taxa of mic…☆24Jul 3, 2021Updated 4 years ago
- R implementation of the LEfSe method☆65Apr 10, 2026Updated last week
- PanTax: Strain-level metagenomic profiling using pangenome graphs☆50Mar 26, 2026Updated 3 weeks ago
- A complete pipeline for metagenomic analysis☆439Apr 10, 2026Updated last week
- ultrafast taxonomic profiling and genome querying for metagenomic samples by abundance-corrected minhash.☆301Feb 3, 2026Updated 2 months ago