Repositories list

• metagenomics-tk

  Public
  The Metagenomics-Toolkit is a scalable, data agnostic workflow that automates the analysis of short and long metagenomic reads obtained from Illumina or Oxford …

  workflowbioinformaticsnanopore+ 3

  workflowbioinformaticsnanoporenextflowmetagenomicsillumina

  Nextflow

  •

  GNU Affero General Public License v3.0

  •55 forks•2828 stars•3737 issues•5656 pull requests•Updated Sep 13, 2026Sep 13, 2026

• submg

  Public
  ENA metagenome upload

  Python

  •

  MIT License

  •11 fork•88 stars•00 issues•00 pull requests•Updated Sep 7, 2026Sep 7, 2026

• long-read-training

  Public
  Long Read Training Course

  1212 forks•00 stars•00 issues•00 pull requests•Updated Jul 9, 2025Jul 9, 2025

• wastewater-study

  Public
  R

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jul 2, 2025Jul 2, 2025

• denbi-nanopore-training

  Public
  de.NBI Nanopore Training Course

  1212 forks•2121 stars•00 issues•44 pull requests•Updated Jun 13, 2025Jun 13, 2025

• prokka

  Public
  :zap: :aquarius: Rapid prokaryotic genome annotation

  Perl

  •236236 forks•00 stars•00 issues•00 pull requests•Updated May 5, 2025May 5, 2025

• metagenomics-workshop

  Public
  1616 forks•88 stars•11 issue•11 pull request•Updated Mar 11, 2025Mar 11, 2025

• 2015-biogas-cebitec

  Public
  Bremges et al. (2015). GigaScience, 4:33.

  TeX

  •

  MIT License

  •66 forks•1212 stars•00 issues•00 pull requests•Updated Dec 29, 2023Dec 29, 2023

• primer-schemes

  Public
  Primer schemes for real-time genome epidemiology

  Python

  •

  Creative Commons Attribution 4.0 International

  •4242 forks•00 stars•00 issues•00 pull requests•Updated Feb 22, 2021Feb 22, 2021

• NanoporeRealTimeAnalysis

  Public
  Java

  •11 fork•00 stars•00 issues•00 pull requests•Updated Jul 25, 2020Jul 25, 2020

• MeRaGENE

  Public
  Python

  •

  MIT License

  •22 forks•44 stars•2323 issues•00 pull requests•Updated Aug 24, 2018Aug 24, 2018

• gru

  Public
  Pipeline for evaluation of 2d Nanopore reads

  HTML

  •00 forks•00 stars•11 issue•00 pull requests•Updated Oct 24, 2017Oct 24, 2017

• cloudcomputing

  Public
  00 forks•00 stars•00 issues•00 pull requests•Updated Jun 16, 2016Jun 16, 2016

• ncbi-genome-download

  Public
  Scripts to download genomes from the NCBI FTP servers

  Python

  •

  Apache License 2.0

  •178178 forks•11 star•00 issues•00 pull requests•Updated May 27, 2016May 27, 2016

• MeCorS

  Public
  Metagenome-enabled error correction of single cell sequencing reads

  C

  •

  MIT License

  •22 forks•00 stars•00 issues•00 pull requests•Updated Mar 24, 2016Mar 24, 2016

• pyani

  Public
  Python module for average nucleotide identity analyses

  Python

  •

  MIT License

  •5757 forks•00 stars•00 issues•00 pull requests•Updated Mar 18, 2016Mar 18, 2016

• PyFlows

  Public
  Generic python workflows, optimized for parallel environments (local server and/or SGE computing cluster)

  Python

  •

  MIT License

  •22 forks•00 stars•00 issues•00 pull requests•Updated Feb 24, 2016Feb 24, 2016

• Mesos

  Public
  Mesos Scheduler Implementations

  Java

  •11 fork•00 stars•22 issues•00 pull requests•Updated Feb 10, 2016Feb 10, 2016

• EG_MinION_2016

  Public
  Edinburgh Genomics MinION training 2016

  1313 forks•00 stars•00 issues•00 pull requests•Updated Feb 3, 2016Feb 3, 2016

• scripts

  Public
  Miscellaneous scripts

  Python

  •

  MIT License

  •1919 forks•11 star•00 issues•00 pull requests•Updated Nov 4, 2015Nov 4, 2015

• sc

  Public
  C

  •11 fork•00 stars•00 issues•00 pull requests•Updated Dec 19, 2014Dec 19, 2014