Repositories list

• biogenome-portal

  Public template
  Biogenome data portal

  taxonomytree-structurebiodiversity

  taxonomytree-structurebiodiversity

  Vue

  •

  MIT License

  •2•6•0•0•Updated Mar 4, 2026Mar 4, 2026

• ebp-assemblies-tracker

  Public
  Tracks the assemblies under the Earth Biogenome Project (PRJNA533106) in NCBI Datasets

  Shell

  •

  MIT License

  •0•1•0•0•Updated Mar 4, 2026Mar 4, 2026

• CLS3_GENCODE

  Public
  Charting thousands of novel gene loci in the human and mouse genomes through targeted full-length long-read RNA sequencing

  R

  •2•4•0•0•Updated Mar 3, 2026Mar 3, 2026

• bioproject-genome-tracker

  Public
  Retrieve all the INSDC public assemblies under a BioProject umbrella

  MIT License

  •2•0•0•0•Updated Mar 1, 2026Mar 1, 2026

• genome-annotation-tracker

  Public
  Tracks Eukaryotic genome annotations (gff) from NCBI and Ensembl

  genomegff3annotations+ 3

  genomegff3annotationsgenesgenomesgff3-files

  Python

  •0•0•0•0•Updated Feb 27, 2026Feb 27, 2026

• BUSCO-tracker

  Public
  Automated BUSCO values for eukaryotic genome annotation

  Python

  •

  MIT License

  •1•0•0•0•Updated Feb 24, 2026Feb 24, 2026

• ansible-role-minknow-guppy-gpu

  Public
  Ansible role to install and configure ONT MinKNOW with GPU support when basecalling using guppy

  0•0•0•0•Updated Jan 26, 2026Jan 26, 2026

• tmerge

  Public
  Merge transcriptome read-to-genome alignments into non-redundant transcript models

  bioinformaticsgenomicsgenome+ 5

  bioinformaticsgenomicsgenomesequencingmergelong-readtranscriptometranscriptomics

  MIT License

  •3•20•1•0•Updated Jan 21, 2026Jan 21, 2026

• grape-nf

  Public
  An automated RNA-seq pipeline using Nextflow

  rna-seqpipelinenextflow+ 3

  rna-seqpipelinenextflowngscrgguigo

  Nextflow

  •

  GNU General Public License v3.0

  •10•37•31•1•Updated Dec 17, 2025Dec 17, 2025

• gffy

  Public
  gffy — A fast GFF statistics extractor. Well, because the world needed another one.

  Python

  •

  MIT License

  •1•0•0•0•Updated Dec 3, 2025Dec 3, 2025

• EPIraction

  Public
  Perl

  •

  GNU General Public License v3.0

  •1•1•0•0•Updated Nov 4, 2025Nov 4, 2025

• jbrowse-plugin-annotrieve

  Public
  Plugin to load annotation tracks from the Annotrieve API

  TypeScript

  •

  Apache License 2.0

  •0•0•0•0•Updated Oct 27, 2025Oct 27, 2025

• LyRic

  Public
  Long RNA-seq analysis workflow

  bioinformaticsrnaseqtranscriptomics+ 4

  bioinformaticsrnaseqtranscriptomicsgencodeclssnakemake-workflowpacbio-iso-seq

  Python

  •

  GNU General Public License v3.0

  •5•22•7•0•Updated Oct 13, 2025Oct 13, 2025

• scientry

  Public template
  Vue

  •0•0•0•0•Updated Jul 28, 2025Jul 28, 2025

• biodiversity-genomics-scripts

  Public
  A bunch of scripts to retrieve biodiversity genomics data (NCBI and Ensembl)

  Python

  •0•0•0•0•Updated Mar 25, 2025Mar 25, 2025

• jbrowse-plugin-refget-api

  Public
  A JBrowse 2 plugin to access servers implementing the refget API of GA4GH

  TypeScript

  •

  Apache License 2.0

  •0•3•0•0•Updated Jan 16, 2025Jan 16, 2025

• gff2ps

  Public
  A program for visualizing annotations of genomic sequences

  Vue

  •0•1•0•0•Updated Oct 25, 2024Oct 25, 2024

• rnaseq-course

  Public
  Data for the RNAseq course at CRG

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

• rnaget-beacon-demo

  Public
  Demo of the RNAget extension for BeaconV2

  Python

  •

  MIT License

  •0•0•0•0•Updated Oct 2, 2024Oct 2, 2024

• beacon-v2

  Public
  Unified repository for the GA4GH Beacon v2 API standard

  Creative Commons Zero v1.0 Universal

  •21•0•0•1•Updated Jul 17, 2024Jul 17, 2024

• ggsashimi

  Public
  Command-line tool for the visualization of splicing events across multiple samples

  Python

  •

  MIT License

  •45•138•9•0•Updated Jun 28, 2024Jun 28, 2024

• file-stream-server

  Public
  A little flask API to stream download files given a folder path

  0•0•0•0•Updated May 14, 2024May 14, 2024

• selenoprofiles-nf

  Public
  selenoprofiles4 nextflow pipeline

  Nextflow

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Jan 7, 2024Jan 7, 2024

• geneidx

  Public
  Nextflow pipeline for genome annotation of protein-coding genes

  genome-annotationgene-predictionnextflow-pipeline

  genome-annotationgene-predictionnextflow-pipeline

  Nextflow

  •

  GNU General Public License v3.0

  •2•16•2•0•Updated Dec 21, 2023Dec 21, 2023

• geneid-parameter-files

  Public
  Repo with all the geneid parameter files

  Python

  •0•0•0•0•Updated Nov 28, 2023Nov 28, 2023

• geneid-param-resolver

  Public
  Given a taxID returns the closest parameter file contained in the repository: https://github.com/guigolab/geneid-parameter-files

  0•0•0•0•Updated Nov 9, 2023Nov 9, 2023

• sqtlseeker2-nf

  Public
  An automated sQTL mapping pipeline using Nextflow

  R

  •

  GNU General Public License v3.0

  •4•7•2•0•Updated Sep 18, 2023Sep 18, 2023

• hugo-future-imperfect-slim

  Public
  Multilingual Blogging Theme for Hugo | Check the Wiki for Documentation

  JavaScript

  •

  Other

  •198•0•0•0•Updated Sep 5, 2023Sep 5, 2023

• sQTLseekeR2

  Public
  R package to detect splicing QTLs (sQTLs)

  R

  •

  GNU General Public License v3.0

  •1•13•1•0•Updated Jul 3, 2023Jul 3, 2023

• spack

  Public
  A flexible package manager that supports multiple versions, configurations, platforms, and compilers.

  Python

  •

  Other

  •2.4k•0•0•0•Updated Jun 30, 2023Jun 30, 2023