EBI-Metagenomics / pipeline-v5View external linksLinks
This repository contains all CWL descriptions of the MGnify pipeline version 5.0.
☆24Oct 3, 2025Updated 4 months ago
Alternatives and similar repositories for pipeline-v5
Users that are interested in pipeline-v5 are comparing it to the libraries listed below
Sorting:
- R/Bioconductor package - STRUCT (STatistics in R Using Class Templates) Toolbox: An extensive set of data (pre-)processing and analysis m…☆11May 21, 2025Updated 8 months ago
- Identify Variants of Concern from metagenomic samples of SARS-CoV-2☆12Sep 9, 2021Updated 4 years ago
- List of companies☆13Dec 24, 2024Updated last year
- t-distributed stochastic neighbor embedding for microbiota data☆12May 12, 2019Updated 6 years ago
- Methods used in the article "Assessment of statistical methods from single cell, bulk RNA-seq and metagenomics applied to microbiome data…☆10Jul 13, 2020Updated 5 years ago
- ☆12Feb 22, 2022Updated 3 years ago
- ☆15Oct 10, 2023Updated 2 years ago
- Biological file format specimens for testing packages, and functions to assist in testing.☆15Nov 18, 2025Updated 2 months ago
- The R package "sarlacc" contains a pipeline to analyse nanopore sequencing data. It trims adapter sequences, retrieves optional UMI's, cl…☆15Feb 27, 2019Updated 6 years ago
- Prioritizing Copy Number Variants (CNV) using Phenotype and Gene Functional Similarity☆17Mar 10, 2022Updated 3 years ago
- Nanopore UMI-linked consensus sequencing☆16Feb 11, 2021Updated 5 years ago
- A Nextflow implementation of the Tuxedo Suite of Tools: HISAT, StringTie & Ballgown☆10Apr 2, 2018Updated 7 years ago
- gutSMASH☆57Oct 3, 2025Updated 4 months ago
- ☆20Feb 4, 2026Updated last week
- Pipeline to filter whole exome vcf files and generate a report document for clinical diagnostics.☆14Nov 11, 2019Updated 6 years ago
- A Snakemake workflow to process single samples or cohorts of Illumina paired-end sequencing data (WGS or WES) using trim galore/bwa/GATK4…☆34Jan 13, 2023Updated 3 years ago
- Handy tools for Microbiome analysis in R☆18May 22, 2019Updated 6 years ago
- motus - a tool for marker gene-based OTU (mOTU) profiling☆169Dec 11, 2025Updated 2 months ago
- Rank-based Gene Ontology analysis of gene expression data☆43Dec 9, 2022Updated 3 years ago
- The Antibiotic Resistance Ontology (ARO) organizes the information describing the ability of a microorganism to withstand the effects of …☆21Oct 2, 2025Updated 4 months ago
- Model-based Genomically Informed High-dimensional Predictor of Microbial Community Metabolic Profiles☆42Mar 26, 2024Updated last year
- Dynamic programming for aa-to-nt alignment with affine gap, splicing and frameshift☆19Sep 30, 2024Updated last year
- ThermoFisher Ion Torrent plugin to detect fetal trisomies and estimate fetal fraction☆17Mar 23, 2018Updated 7 years ago
- Data processing and analysis scripts for our spatial profiling of embryos using seqFISH☆16Feb 10, 2023Updated 3 years ago
- H3ABioNet 16S rDNA diverstity analysis package☆19May 20, 2019Updated 6 years ago
- k-mer similarity analysis pipeline☆22Nov 20, 2025Updated 2 months ago
- This repository contains the CWL description of the EBI Metagenomics pipeline☆21Apr 7, 2021Updated 4 years ago
- Create graphs from DokuWiki link structures☆20May 13, 2022Updated 3 years ago
- R package for Statistical Inference of Associations between Microbial Communities And host phenoType☆58Jan 30, 2024Updated 2 years ago
- Amplicon sequence processing workflow using QIIME 2 and Snakemake☆45Dec 22, 2025Updated last month
- ☆11Jul 3, 2022Updated 3 years ago
- myVCF: a web-based platform for target and exome mutations data management☆20Apr 13, 2021Updated 4 years ago
- Improvement of metagenome-assembled genomes☆54Mar 17, 2020Updated 5 years ago
- Simple R utilities for working with HMMER☆19Oct 3, 2024Updated last year
- Toolkit for establishing, updating, and validating GTDB species clusters☆20Oct 22, 2025Updated 3 months ago
- Annotation of Metabolite Origin via Networks: A tool for predicting putative metabolite origins for microbes or between microbes and host…☆25Jan 15, 2026Updated last month
- ☆22Sep 17, 2025Updated 5 months ago
- Gene Ontology subgraph visualizations☆20Jan 6, 2026Updated last month
- Course materials for the Genomics Aotearoa Metagenomics Summer School, to be hosted at the University of Auckland in Septermber☆68Sep 5, 2024Updated last year