Repositories list

• PhD_course_genomics_format

  Public
  PhD course about genomics format

  bioinformaticsgenomics

  Shell

  •1•0•0•0•Updated Oct 17, 2025Oct 17, 2025

• pacvar

  Public
  Longread PacBio sequencing processing for WGS and PureTarget

  Nextflow

  •

  MIT License

  •9•0•0•0•Updated Oct 17, 2025Oct 17, 2025

• Bionextflow3

  Public
  Collection of modules

  Nextflow

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Oct 9, 2025Oct 9, 2025

• bca-website

  Public
  Biodiversity Cell Atlas website and data portal

  HTML

  •

  Apache License 2.0

  •1•0•0•0•Updated Sep 30, 2025Sep 30, 2025

• BioNextflow

  Public
  A collection of modules and sub-workflows for Nextflow

  librarybioinformaticstools+ 2pipelinenextflow

  Nextflow

  •

  GNU General Public License v3.0

  •5•28•6•1•Updated Sep 29, 2025Sep 29, 2025

• sphinx-bioschemas

  Public
  A Sphinx extension to include Bioschemas

  sphinxschema-orgsphinx-extension+ 1bioschemas

  Python

  •

  MIT License

  •0•0•0•0•Updated Aug 27, 2025Aug 27, 2025

• Genome-Browser-Course

  Public
  genome-browser

  MIT License

  •0•0•0•0•Updated Aug 26, 2025Aug 26, 2025

• openst

  Public
  Open-ST: profile and analyze tissue transcriptomes in 3D with high resolution in your lab

  HTML

  •

  Other

  •20•0•0•0•Updated Aug 22, 2025Aug 22, 2025

• docker-debian-perlbrew

  Public
  Basic Docker image for running Debian with perlbrew installed

  Dockerfile

  •1•3•0•0•Updated Jul 17, 2025Jul 17, 2025

• master_of_pores

  Public
  Nextflow pipeline for analysis of direct RNA Nanopore reads

  dockernextflowsingularity+ 3nanopore-sequencingnextflow-pipelinenanopore-analysis-pipeline

  Nextflow

  •

  MIT License

  •18•108•2•0•Updated Jun 23, 2025Jun 23, 2025

• allele_specific_RNAseq

  Public
  Allele Specific RNAseq

  Nextflow

  •2•11•1•1•Updated May 26, 2025May 26, 2025

• NGS-QC-Course

  Public
  ngsbioinfomatics

  MIT License

  •0•0•0•0•Updated May 12, 2025May 12, 2025

• nextflow-course-2025-spring

  Public
  Nextflow course

  Nextflow

  •

  MIT License

  •6•2•0•0•Updated Apr 25, 2025Apr 25, 2025

• docker-amazonlinux-perlbrew

  Public
  Basic Docker image for running AmazonLinux with perlbrew installed

  Dockerfile

  •3•0•0•0•Updated Feb 12, 2025Feb 12, 2025

• docker-almalinux-perlbrew

  Public
  Images for running Perlbrew scripts using Almalinux.

  0•0•0•0•Updated Feb 8, 2025Feb 8, 2025

• interproscan_docker

  Public
  Docker recipe for building Interproscan

  Dockerfile

  •

  MIT License

  •2•1•0•0•Updated Jan 14, 2025Jan 14, 2025

• ExOrthist

  Public
  ExOrthist: a pipeline to extract exon orthologies at any evolutionary distance.

  Nextflow

  •

  MIT License

  •4•26•5•0•Updated Dec 5, 2024Dec 5, 2024

• MoP3

  Public
  Master of Pores SSJ3

  R

  •

  MIT License

  •1•2•15•0•Updated Dec 4, 2024Dec 4, 2024

• MOP2

  Public
  Master of Pores 2

  dockerrna-seqnanopore+ 5pipelinenextflowsingularityrnacdna

  Nextflow

  •

  MIT License

  •8•23•21•0•Updated Dec 4, 2024Dec 4, 2024

• PhD_course_containers_2024

  Public
  Scientific Containers CRG PhD Course 2024

  dockercontainerssingularity+ 2podmanapptainer

  Python

  •3•0•0•0•Updated Oct 21, 2024Oct 21, 2024

• .github

  Public
  0•0•0•0•Updated Sep 4, 2024Sep 4, 2024

• docker-centos-legacy-perlbrew

  Public archive
  Legacy repository for CentOS 7 Docker builds

  Dockerfile

  •0•0•0•0•Updated Jul 8, 2024Jul 8, 2024

• nextflow-course-2024-alba

  Public
  Nextflow course for ALBA - 2024

  dockernextflowcontainers+ 2singularityapptainer

  Python

  •

  MIT License

  •6•2•0•0•Updated Feb 9, 2024Feb 9, 2024

• bioconda-recipes

  Public
  Conda recipes for the bioconda channel.

  Shell

  •

  MIT License

  •3.6k•0•0•0•Updated Jan 9, 2024Jan 9, 2024

• contamination-nf

  Public
  Nextflow pipeline for checking contamination problems with reads among other tasks

  Nextflow

  •

  MIT License

  •0•0•2•0•Updated Dec 7, 2023Dec 7, 2023

• PhD_course_genomics_format_2023

  Public archive
  PhD course about genomics format 2023

  1•0•0•0•Updated Oct 17, 2023Oct 17, 2023

• PhD_course_containers_2023

  Public
  Scientific Containers CRG PhD Course 2023

  dockercontainerssingularity

  Python

  •3•0•0•0•Updated Oct 16, 2023Oct 16, 2023

• transcriptome_assembly

  Public
  Biocore's de novo transcriptome assembly workflow based on Nextflow

  denovo-assemblytranscriptome-assembly

  Nextflow

  •2•3•1•0•Updated Oct 5, 2023Oct 5, 2023

• nextflow-course-2023-fall

  Public
  Nextflow course

  nextflowcontainers

  Nextflow

  •

  MIT License

  •6•2•0•0•Updated Sep 13, 2023Sep 13, 2023

• biocorecrg.github.io

  Public
  CRG's Bioinformatics Core facility GitHub web-page

  HTML

  •1•0•0•0•Updated Sep 12, 2023Sep 12, 2023