Repositories list

• mgnify-ro-crates

  Public
  A library for creating browsable ro-crates for various pipeline results

  Python

  •

  Other

  •0•0•0•0•Updated Nov 16, 2024Nov 16, 2024

• mett-dataportal

  Public
  Python

  •0•0•0•0•Updated Nov 15, 2024Nov 15, 2024

• containers

  Public
  Repository to contain containers used by EBI Microbiome Informatics

  Python

  •0•0•0•1•Updated Nov 15, 2024Nov 15, 2024

• miassembler

  Public
  Nextflow

  •

  Apache License 2.0

  •0•1•0•0•Updated Nov 15, 2024Nov 15, 2024

• HoloFoodR

  Public
  R interface for HoloFood resource

  R

  •

  Artistic License 2.0

  •1•1•3•1•Updated Nov 15, 2024Nov 15, 2024

• mgnify-pipelines-toolkit

  Public
  Python

  •

  Apache License 2.0

  •1•0•0•0•Updated Nov 15, 2024Nov 15, 2024

• hmmer3

  Public
  HMMER (version 3) related projects

  C

  •0•1•0•0•Updated Nov 15, 2024Nov 15, 2024

• genomes-generation

  Public
  Nextflow

  •

  Apache License 2.0

  •0•2•0•1•Updated Nov 15, 2024Nov 15, 2024

• fetch_tool

  Public
  Tool which allows you to fetch RAW read files from the European Nucleotide Archive (ENA)

  Python

  •

  Apache License 2.0

  •2•2•4•1•Updated Nov 14, 2024Nov 14, 2024

• taxdb_generation_nf

  Public
  Perl

  •

  Apache License 2.0

  •0•0•0•0•Updated Nov 14, 2024Nov 14, 2024

• genomes-catalogue-pipeline

  Public
  MGnify genome analysis pipeline

  Python

  •

  Other

  •21•101•7•2•Updated Nov 14, 2024Nov 14, 2024

• microeuks-gene-benchmarker

  Public
  Scripts to benchmark the outputs from gene annotation tools for microbial eukaryotes

  Nextflow

  •

  Apache License 2.0

  •0•0•0•0•Updated Nov 14, 2024Nov 14, 2024

• deciphon

  Public
  Deciphon related projects

  C

  •0•0•0•0•Updated Nov 12, 2024Nov 12, 2024

• mettannotator

  Public
  Python

  •

  Apache License 2.0

  •5•57•2•1•Updated Nov 12, 2024Nov 12, 2024

• deciphon_web

  Public
  React webapp to submit and retrieve jobs from Deciphon – a protein prediction tool for nanopore reads

  reactprotein-annotationnanopore-sequencing

  JavaScript

  •

  Apache License 2.0

  •1•0•0•1•Updated Nov 11, 2024Nov 11, 2024

• emg-viral-pipeline

  Public
  VIRify: detection of phages and eukaryotic viruses from metagenomic and metatranscriptomic assemblies

  workflowpipelinenextflow+ 2virusescwl

  Python

  •

  Apache License 2.0

  •16•128•20•1•Updated Nov 8, 2024Nov 8, 2024

• ro-crate-browser

  Public
  A standalone library for browsing ro crates.

  TypeScript

  •0•0•0•0•Updated Nov 8, 2024Nov 8, 2024

• vue-ro-crate-browser

  Public
  A Vue js library for browsing self contained ro-crates

  TypeScript

  •0•0•0•0•Updated Nov 8, 2024Nov 8, 2024

• react-ro-crate-browser

  Public
  A standalone library for browsing ro crates.

  TypeScript

  •0•0•0•0•Updated Nov 7, 2024Nov 7, 2024

• amplicon-pipeline

  Public
  Nextflow

  •

  Apache License 2.0

  •1•4•0•0•Updated Nov 6, 2024Nov 6, 2024

• emgapi

  Public
  MGnify RESTful API

  apidjangoresource+ 2django-rest-frameworkjsonapi

  Python

  •

  Apache License 2.0

  •0•10•5•7•Updated Nov 6, 2024Nov 6, 2024

• lite-pack

  Public
  C library implementing the MessagePack serialisation format.

  C

  •

  MIT License

  •0•0•0•0•Updated Nov 5, 2024Nov 5, 2024

• ebi-metagenomics-client

  Public
  This repos contains the MGnify web client

  javascriptclientwebsite+ 2webpackbackbone

  TypeScript

  •1•4•0•10•Updated Nov 4, 2024Nov 4, 2024

• MAG-to-assembly-pipeline

  Public
  Nextflow pipeline that wraps the assembly-MAG linking script

  0•0•0•1•Updated Nov 4, 2024Nov 4, 2024

• motus_pipeline

  Public
  Raw reads mOTUs and taxonomic classification pipeline

  HTML

  •

  Apache License 2.0

  •0•3•0•0•Updated Nov 4, 2024Nov 4, 2024

• kegg-pathways-completeness-tool

  Public
  Python

  •

  Apache License 2.0

  •3•15•1•4•Updated Nov 1, 2024Nov 1, 2024

• MGnifyR

  Public
  R package for searching, downloading and analysis of EBI MGnify metagenomics data

  R

  •

  Artistic License 2.0

  •10•19•4•0•Updated Oct 31, 2024Oct 31, 2024

• assembly_uploader

  Public
  Upload of metagenome and metatranscriptome assemblies to ENA

  Python

  •

  Apache License 2.0

  •0•0•0•0•Updated Oct 31, 2024Oct 31, 2024

• mgnifams

  Public
  Python

  •

  Apache License 2.0

  •0•1•0•0•Updated Oct 24, 2024Oct 24, 2024

• pipeline-v5

  Public
  This repository contains all CWL descriptions of the MGnify pipeline version 5.0.

  workflowmetagenomicscommon-workflow-language+ 10cwlmetagenomic-analysismetagenomic-classificationmetagenomic-dataamplicon-pipelinecwl-workflowcwl-descriptions+ 3

  HTML

  •

  Apache License 2.0

  •20•22•3•0•Updated Oct 24, 2024Oct 24, 2024