Repositories list

• mapto

  Public
  Map reads to random stuff using bowtie2

  Shell

  •0•0•0•0•Updated Mar 19, 2024Mar 19, 2024

• cdhit

  Public
  Automatically exported from code.google.com/p/cdhit

  Perl

  •

  GNU General Public License v2.0

  •129•0•0•0•Updated Mar 2, 2023Mar 2, 2023

• sarscov2-epidemiology

  Public archive
  Visualisation of SARS-CoV-2 genomic epidemiology

  visualisationdatasetestonia+ 2auspicesars-cov-2

  Python

  •

  MIT License

  •0•0•0•0•Updated Feb 20, 2023Feb 20, 2023

• minced

  Public
  Mining CRISPRs in Environmental Datasets

  Java

  •

  GNU General Public License v3.0

  •17•0•0•0•Updated Feb 10, 2023Feb 10, 2023

• virome-wrappers

  Public
  snakemake wrappers

  snakemakewrappers

  Python

  •

  MIT License

  •0•1•0•0•Updated Apr 11, 2022Apr 11, 2022

• blast-virome

  Public
  Virome taxonomic profiling using BLAST

  Python

  •0•0•0•0•Updated Mar 21, 2022Mar 21, 2022

• snakemake-wrappers

  Public
  This is the development home of the Snakemake wrapper repository, see

  Python

  •186•0•0•0•Updated Mar 16, 2022Mar 16, 2022

• sarscov2-variation

  Public
  SARS-CoV-2 sequencing workflow

  snakemake-workflowcovid-19sars-cov-2+ 7covid-19-estoniakorogeno-estworkflowsnakemakeconsensus-sequencessnakefilesarscov2-variation

  Python

  •

  MIT License

  •0•2•0•0•Updated Jan 26, 2022Jan 26, 2022

• discover-virome

  Public
  discover-virome: identify and quantify viruses from metagenomic assemblies

  snakemakeviromemetagenomic-analysis+ 3metagenomic-classificationsnakemake-workflowvirome-workflow

  Python

  •

  MIT License

  •1•3•0•1•Updated Jan 20, 2022Jan 20, 2022

• metaTOR

  Public
  Metagenomic binning based on Hi-C data

  Python

  •

  GNU General Public License v3.0

  •10•0•0•0•Updated Jan 10, 2022Jan 10, 2022

• DMP

  Public
  Codes and sample data supporting the Dutch Microbiome Project. The preprint is currently available at https://www.biorxiv.org/content/10.1101/2020.11.27.401125v1 and full data can be requested from EGA (https://ega-archive.org/studies/EGAS00001005027) and Lifelines biobank (https://www.lifelines.nl/researcher)

  HTML

  •18•0•0•0•Updated Jun 24, 2021Jun 24, 2021

• ena-upload-cli

  Public
  Python

  •

  MIT License

  •15•0•0•0•Updated Apr 30, 2021Apr 30, 2021

• ena-upload

  Public
  Snakemake workflow to upload Sars-Cov-2 reads to ENA

  snakemakeuploadena+ 5snakemake-workflowsars-cov-2covid-19-estoniasnakefilekorogeno-est

  Python

  •

  MIT License

  •0•3•0•0•Updated Apr 26, 2021Apr 26, 2021

• galaxy-api-scripts

  Public
  Ad hoc scripts to run ARTIC COVID19 Galaxy workflows

  galaxycovid19bioblend+ 1articv3

  Python

  •

  MIT License

  •0•0•0•0•Updated Apr 14, 2021Apr 14, 2021

• ampliseq

  Public
  16S rRNA amplicon sequencing analysis workflow using QIIME2

  Nextflow

  •

  MIT License

  •117•0•0•0•Updated Mar 31, 2021Mar 31, 2021

• dadasnake

  Public
  Amplicon sequencing workflow heavily using DADA2 and implemented in snakemake

  Python

  •

  GNU General Public License v3.0

  •19•0•0•0•Updated Mar 14, 2021Mar 14, 2021

• tools-iuc

  Public
  Tool Shed repositories maintained by the Intergalactic Utilities Commission

  HTML

  •

  MIT License

  •430•0•0•0•Updated Feb 4, 2021Feb 4, 2021

• prokka

  Public
  ⚡ ♒ Rapid prokaryotic genome annotation

  Perl

  •226•0•0•0•Updated Aug 24, 2020Aug 24, 2020

• emg-viral-pipeline

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

  Nextflow

  •

  Apache License 2.0

  •16•0•0•0•Updated Aug 10, 2020Aug 10, 2020

• quantify-virome

  Public
  quantify-virome: identify and quantify viruses from metagenomic shotgun sequences

  metagenomicsviromesnakemake-workflows+ 4metagenomic-pipelinesnakemaketaxonomyvirome-workflow

  Python

  •

  MIT License

  •1•3•0•0•Updated May 29, 2020May 29, 2020

• artic-ncov2019

  Public
  ARTIC nanopore protocol for nCoV2019 novel coronavirus

  Creative Commons Attribution 4.0 International

  •165•0•0•0•Updated Mar 24, 2020Mar 24, 2020

• sars-covid-2-ncbi

  Public
  Download sars-covid-2 sequencing runs from NCBI

  Python

  •

  MIT License

  •0•0•0•0•Updated Mar 16, 2020Mar 16, 2020

• p-dip

  Public
  Pathogen discovery pipeline (p-dip)

  Python

  •2•0•0•0•Updated Feb 6, 2020Feb 6, 2020

• quast-singularity

  Public
  QUAST singularity image

  MIT License

  •0•0•0•0•Updated Jan 14, 2020Jan 14, 2020

• singularity-cdhit

  Public
  CD-HIT suite singularity image

  singularity-containercd-hit

  MIT License

  •0•0•0•0•Updated Jan 14, 2020Jan 14, 2020

• metformin-virome

  Public
  R

  •

  MIT License

  •0•0•0•0•Updated Dec 17, 2019Dec 17, 2019

• phageterm

  Public
  Phageterm fork of the code that is available via sourceforge

  Python

  •2•0•0•0•Updated Nov 15, 2019Nov 15, 2019

• discover-profile

  Public
  Snakemake HPC cluster profile for discover-virome workflow

  Python

  •0•0•0•0•Updated Nov 15, 2019Nov 15, 2019

• Demovir

  Public
  Taxonomic classification of viruses at Order and Family level

  R

  •9•0•0•0•Updated Nov 6, 2019Nov 6, 2019

• virus-contigs-annotation

  Public
  Virus contig annotation workflow

  Python

  •

  MIT License

  •0•0•0•0•Updated Oct 29, 2019Oct 29, 2019