Repositories list

• Training-Tech-shorts

  Public
  Short lessons, training various technologies useful to our work.

  TeX

  •12•4•20•1•Updated Feb 13, 2025Feb 13, 2025

• bp-sweden-web

  Public
  Website for BigPicture Sweden

  SCSS

  •

  MIT License

  •0•0•1•1•Updated Feb 13, 2025Feb 13, 2025

• elixir_evaluation_evaluation

  Public
  An evaluation of the ELIXIR course evaluation

  elixircourseevaluation+ 2surveynbis

  Shell

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Feb 13, 2025Feb 13, 2025

• data-submission-documentation

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

  Python

  •0•3•0•6•Updated Feb 13, 2025Feb 13, 2025

• MrBayes

  Public
  MrBayes is a program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models. For documentation and downloading the program, please see the home page:

  bioinformaticsphylogeneticsresearch-tool+ 2bayesian-inferencemarkov-chain-monte-carlo

  C

  •

  GNU General Public License v3.0

  •80•239•72•0•Updated Feb 13, 2025Feb 13, 2025

• AGAT

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

  toolkitperl-scriptsgtf+ 4gffagatstandardisationgff-format

  Perl

  •

  GNU General Public License v3.0

  •57•480•18•0•Updated Feb 12, 2025Feb 12, 2025

• sda-services-backup

  Public
  neic-sda

  Go

  •1•2•1•0•Updated Feb 12, 2025Feb 12, 2025

• fungal-trans

  Public
  A Snakemake workflow for fungal metatranscriptomics

  Python

  •

  MIT License

  •4•4•1•0•Updated Feb 11, 2025Feb 11, 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•64•2•Updated Feb 11, 2025Feb 11, 2025

• NanoSeq

  Public
  Analysis software for Nanorate Sequencing (NanoSeq) experiments

  C++

  •

  GNU Affero General Public License v3.0

  •10•0•0•0•Updated Feb 11, 2025Feb 11, 2025

• sdafs

  Public
  FUSE file system driver for the sensitive data archive

  Go

  •

  MIT License

  •0•0•0•1•Updated Feb 10, 2025Feb 10, 2025

• sda-uppmax-integration

  Public
  Go

  •0•0•0•0•Updated Feb 10, 2025Feb 10, 2025

• sda-cli

  Public
  User command line interface for the SDA

  Go

  •

  GNU Affero General Public License v3.0

  •1•5•51•0•Updated Feb 10, 2025Feb 10, 2025

• urdr

  Public
  Timelogging system of NBIS

  TypeScript

  •

  GNU Affero General Public License v3.0

  •1•0•57•22•Updated Feb 8, 2025Feb 8, 2025

• strobealign-evaluation

  Public
  Python

  •0•0•0•0•Updated Feb 7, 2025Feb 7, 2025

• workshop-scRNAseq-devel

  Public
  Single cell RNA sequencing analysis course

  HTML

  •101•0•3•0•Updated Feb 7, 2025Feb 7, 2025

• ceph_utils

  Public
  Various scripts used to setup and interact with a Ceph cluster

  Shell

  •0•1•0•0•Updated Feb 6, 2025Feb 6, 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

  •2•3•4•3•Updated Feb 6, 2025Feb 6, 2025

• aida-genai-workshop

  Public
  Workshop files for the AIDA Data Hub Generative AI workshop

  Python

  •

  MIT License

  •1•0•0•0•Updated Feb 6, 2025Feb 6, 2025

• workshop-reproducible-research

  Public
  NBIS/Elixir course: Tools for Reproducible Research

  HTML

  •

  Creative Commons Attribution 4.0 International

  •32•63•7•0•Updated Feb 5, 2025Feb 5, 2025

• bp-landing-pages

  Public
  Bigpicture project dataset landing page generator

  HTML

  •0•0•0•0•Updated Feb 4, 2025Feb 4, 2025

• teaching_literature_club

  Public
  NBIS' teaching literature club

  clubmeetingteaching+ 2literaturenbis

  Shell

  •

  GNU General Public License v3.0

  •1•0•0•0•Updated Feb 3, 2025Feb 3, 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•16•2•Updated Feb 3, 2025Feb 3, 2025

• nbis-webapp

  Public
  Hosting service for NBIS web applications during development

  Shell

  •

  MIT License

  •0•0•0•0•Updated Jan 31, 2025Jan 31, 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•11•0•Updated Jan 30, 2025Jan 30, 2025

• workshop-mlbiostatistics

  Public
  HTML

  •8•15•0•0•Updated Jan 30, 2025Jan 30, 2025

• predictprotein-webserver-topcons2

  Public
  web-server implementation for topcons2

  HTML

  •

  MIT License

  •0•1•14•4•Updated Jan 29, 2025Jan 29, 2025

• harbor-helm

  Public
  Harbor helm chart for BP AI registry

  Mustache

  •

  Apache License 2.0

  •765•0•0•0•Updated Jan 27, 2025Jan 27, 2025

• module-metadata-dm-practices

  Public
  Metadata module for Data Management course (carpentries style)

  Ruby

  •

  Other

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