Repositories list

• sda-cli

  Public
  User command line interface for the SDA

  Go

  •

  GNU Affero General Public License v3.0

  •1•5•51•3•Updated Jan 27, 2025Jan 27, 2025

• bp-landing-pages

  Public
  Bigpicture project dataset landing page generator

  HTML

  •0•0•0•1•Updated Jan 27, 2025Jan 27, 2025

• teaching_literature_club

  Public
  NBIS' teaching literature club

  clubmeetingteaching+ 2literaturenbis

  Shell

  •

  GNU General Public License v3.0

  •1•0•0•0•Updated Jan 26, 2025Jan 26, 2025

• sdafs

  Public
  FUSE file system driver for the sensitive data archive

  Go

  •

  MIT License

  •0•0•0•0•Updated Jan 24, 2025Jan 24, 2025

• GenErode

  Public
  GitHub repository for GenErode, a Snakemake pipeline for the analysis of whole-genome sequencing data from historical and modern samples to study patterns of genome erosion.

  Python

  •

  GNU General Public License v3.0

  •7•25•15•2•Updated Jan 24, 2025Jan 24, 2025

• nf-core-aMeta

  Public
  An nf-core compliant version of aMeta; An ancient metagenomic profiling Snakemake workflow

  Nextflow

  •

  MIT License

  •2•1•1•2•Updated Jan 24, 2025Jan 24, 2025

• sda-services-backup

  Public
  neic-sda

  Go

  •1•2•1•0•Updated Jan 24, 2025Jan 24, 2025

• NanoSeq-fork

  Public
  Analysis software for Nanorate Sequencing (NanoSeq) experiments

  C++

  •

  GNU Affero General Public License v3.0

  •10•0•0•0•Updated Jan 24, 2025Jan 24, 2025

• workshop-ngsintro

  Public
  Workshop • Intro to Bioinformatics using NGS data • 5 days

  rnaseqvariant-callingunix-shell+ 2ngs-analysisbioinformatics

  HTML

  •

  GNU General Public License v3.0

  •7•14•0•0•Updated Jan 24, 2025Jan 24, 2025

• raukr-2025

  Public
  Raukr 2025 • NBIS Summer School • R Beyond the Basics

  trainingworkshopr-programming+ 3nbisr-codenbisweden

  Lua

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Jan 24, 2025Jan 24, 2025

• raukr

  Public
  RaukR • R Beyond The Basics

  courseworkshopr-programming+ 3quartoraukrr-course

  SCSS

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Jan 24, 2025Jan 24, 2025

• elixir_evaluation_evaluation

  Public
  An evaluation of the ELIXIR course evaluation

  GNU General Public License v3.0

  •0•0•0•0•Updated Jan 24, 2025Jan 24, 2025

• workshop-reproducible-research

  Public
  NBIS/Elixir course: Tools for Reproducible Research

  HTML

  •

  Creative Commons Attribution 4.0 International

  •32•62•8•0•Updated Jan 23, 2025Jan 23, 2025

• workshop-data-visualization-r

  Public
  Materials for NBIS workshop on data visulalization

  visualizationworkshopdata-visualization

  HTML

  •

  GNU General Public License v3.0

  •2•2•2•0•Updated Jan 23, 2025Jan 23, 2025

• sda-uppmax-integration

  Public
  Go

  •0•0•0•0•Updated Jan 23, 2025Jan 23, 2025

• workshop-scRNAseq-devel

  Public
  Single cell RNA sequencing analysis course

  HTML

  •101•0•3•0•Updated Jan 22, 2025Jan 22, 2025

• harbor-helm

  Public
  Harbor helm chart for BP AI registry

  Mustache

  •

  Apache License 2.0

  •766•0•0•0•Updated Jan 22, 2025Jan 22, 2025

• PLP_Design_Portal

  Public
  This repository contains a package to create padlock probes that target RNA directly and for developing a user-friendly.portal

  0•0•12•1•Updated Jan 22, 2025Jan 22, 2025

• CMK-NBIS-PRT-project-template

  Public template
  NBIS peer review track project template

  0•1•0•0•Updated Jan 21, 2025Jan 21, 2025

• bp-sweden-web

  Public
  Website for BigPicture Sweden

  SCSS

  •

  MIT License

  •0•0•1•2•Updated Jan 20, 2025Jan 20, 2025

• Earth-Biogenome-Project-pilot

  Public
  Assembly and Annotation workflows for analysing data in the Earth Biogenome Project pilot project.

  Nextflow

  •

  GNU General Public License v3.0

  •8•12•57•1•Updated Jan 20, 2025Jan 20, 2025

• AGAT

  Public
  Another Gtf/Gff Analysis Toolkit https://nbisweden.github.io/AGAT/

  toolkitperl-scriptsgtf+ 4gffagatstandardisationgff-format

  Perl

  •

  GNU General Public License v3.0

  •58•477•18•0•Updated Jan 20, 2025Jan 20, 2025

• Sloppymerase

  Public
  Find single-stranded DNA breaks with an error-prone DNA polymerase

  Python

  •

  MIT License

  •0•0•0•0•Updated Jan 17, 2025Jan 17, 2025

• PLUPP-sv-mock-server

  Public
  A mock server to improve development experience for SV apps

  JavaScript

  •0•1•0•0•Updated Jan 15, 2025Jan 15, 2025

• theherdbook

  Public
  The Herd Book

  studbokherd-managementgenebank+ 1herd-book

  TypeScript

  •

  GNU Affero General Public License v3.0

  •1•1•30•26•Updated Jan 15, 2025Jan 15, 2025

• data-submission-documentation

  Public
  Documentation for data submissions from life science research in public repositories

  Python

  •0•3•0•4•Updated Jan 14, 2025Jan 14, 2025

• assembly-project-template

  Public template
  This is a template for all assembly projects. Please read the instructions below on how to use it.

  project-templategenome-annotationgenome-analysis+ 1genome-assembly

  Shell

  •

  MIT License

  •1•3•3•2•Updated Jan 13, 2025Jan 13, 2025

• fungal-trans

  Public
  A Snakemake workflow for fungal metatranscriptomics

  Python

  •

  MIT License

  •4•4•1•0•Updated Jan 13, 2025Jan 13, 2025

• confluence-server-to-cloud-utils

  Public
  Various scripts used when migrating a Confluence Server instance to a Confluence Cloud instance.

  Python

  •0•2•0•0•Updated Jan 9, 2025Jan 9, 2025

• NBIS-support-framework

  Public template
  A framework for support projects, including templates for reports, data management as well as links to tools and pipelines

  0•8•0•0•Updated Jan 9, 2025Jan 9, 2025