Simple statistical identification and removal of contaminants in marker-gene and metagenomics sequencing data
☆174Sep 4, 2025Updated 10 months ago
Alternatives and similar repositories for decontam
Users that are interested in decontam are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Accurate sample inference from amplicon data with single nucleotide resolution☆554Feb 13, 2026Updated 5 months ago
- Differential abundance (DA) and correlation analyses for microbial absolute abundance data☆142Apr 27, 2026Updated 2 months ago
- 🌈 Interactive analysis of metagenomics data☆454Sep 17, 2025Updated 10 months ago
- Code, unit tests, and tutorials for running PICRUSt2☆394Nov 27, 2025Updated 8 months ago
- diversity estimation under ecological networks☆83Jun 16, 2026Updated last month
- Bare Metal GPUs on DigitalOcean Gradient AI • AdPurpose-built for serious AI teams training foundational models, running large-scale inference, and pushing the boundaries of what's possible.
- Species richness with high diversity☆68Jun 25, 2026Updated last month
- Predicting Absolute and Relative Abundance by Modeling Efficiency to Derive Intervals and Concentrations☆15Nov 24, 2025Updated 8 months ago
- Amplicon sequencing pipelines suitable for SSU (16S, 18S), LSU (23S, 28S) and ITS.☆54Jun 14, 2025Updated last year
- KrakenTools provides individual scripts to analyze Kraken/Kraken2/Bracken/KrakenUniq output files☆382Aug 1, 2025Updated 11 months ago
- R package for microbiome biomarker discovery☆200Feb 19, 2025Updated last year
- Speedy versions of phyloseq functions☆48Apr 21, 2024Updated 2 years ago
- An integrated pipeline for estimating strain-level genomic variation from metagenomic data☆135Oct 6, 2023Updated 2 years ago
- SHallow shOtGUN profiler☆52Mar 4, 2022Updated 4 years ago
- 🐙 KrakenUniq: Metagenomics classifier with unique k-mer counting for more specific results☆252Jan 18, 2024Updated 2 years ago
- Deploy to Railway using AI coding agents - Free Credits Offer • AdUse Claude Code, Codex, OpenCode, and more. Autonomous software development now has the infrastructure to match with Railway.
- Import qiime2 artifacts to R☆183Dec 12, 2024Updated last year
- phyloseq is a set of classes, wrappers, and tools (in R) to make it easier to import, store, and analyze phylogenetic sequencing data; an…☆650Feb 27, 2026Updated 4 months ago
- ☆33Jan 4, 2025Updated last year
- Create BIOM-format tables (http://biom-format.org) from Kraken output (http://ccb.jhu.edu/software/kraken/, https://github.com/DerrickWoo…☆61Feb 7, 2026Updated 5 months ago
- Experimental pipeline to perform de novo PICRUSt on de-noised amplicon sequence variants (ASV)☆19Oct 23, 2018Updated 7 years ago
- FishTaco (Functional Shifts Taxonomic Contributors) is a metagenomic computational framework that aims to identify the driver taxa of mic…☆24Jul 3, 2021Updated 5 years ago
- A comprehensive R package for deep mining microbiome☆195Apr 29, 2026Updated 2 months ago
- An R package for removing contamination from metabarcoding (e.g., microbiome) datasets post-sequencing☆21Oct 17, 2023Updated 2 years ago
- Precise phylogenetic analysis of microbial isolates and genomes from metagenomes☆169Jun 10, 2026Updated last month
- Deploy on Railway without the complexity - Free Credits Offer • AdConnect your repo and Railway handles the rest with instant previews. Quickly provision container image services, databases, and storage volumes.
- High-resolution strain-level microbiome composition analysis tool based on reference genomes and k-mers☆44Apr 8, 2024Updated 2 years ago
- Track, Analyze, Visualize: Unravel Your Microbiome's Temporal Pattern with MicrobiomeStat☆50Jun 6, 2026Updated last month
- Sparse InversE Covariance estimation for Ecological Association and Statistical Inference☆233Apr 29, 2026Updated 2 months ago
- A repository of bioinformatic scripts, SOPs, and tutorials for analyzing microbiome data.☆460Feb 13, 2026Updated 5 months ago
- strain-level analysis tools☆41Oct 21, 2024Updated last year
- Microbial analysis in TCGA data☆94Feb 23, 2024Updated 2 years ago
- SourceTracker2☆92Jul 10, 2024Updated 2 years ago
- microbiome R package☆318May 12, 2026Updated 2 months ago
- The second version of the Kraken taxonomic sequence classification system☆926Updated this week
- GPUs on demand by Runpod - Special Offer Available • AdRun AI, ML, and HPC workloads on powerful cloud GPUs—without limits or wasted spend. Deploy GPUs in under a minute and pay by the second.
- A user-friendly workflow for phylogenomics☆231Updated this week
- Orchestrating Microbiome Analysis☆109Jul 10, 2026Updated 2 weeks ago
- Distilled and Refined Annotation of Metabolism: A tool for the annotation and curation of function for microbial and viral genomes☆335Updated this week
- A robust, extensible metagenomics pipeline☆177Jul 20, 2026Updated last week
- Core ELEment Bias Removal In Metagenome Binned ORthologs: A pipeline to make pangenomes from MAGs☆26Jul 22, 2024Updated 2 years ago
- Various customs functions written to enhance the base functions of phyloseq. Most of them are used in the formation "Métagénomique 16S" p…☆33Oct 29, 2025Updated 8 months ago
- DAS Tool☆177May 2, 2024Updated 2 years ago