Repositories list

• varvis-download

  Public
  A CLI tool to download genomic analysis files from the Varvis API. Supports authentication, file type selection, proxy settings, and destination directory specification.

  apiclinode+ 6bioinformaticsauthenticationgenomicsproxy-supportdata-downloadvarvis

  JavaScript

  •

  GNU General Public License v3.0

  •0•1•3•0•Updated Oct 18, 2024Oct 18, 2024

• chatgpt-mattermost-bot

  Public
  A very simple implementation of a service for a mattermost bot that uses ChatGPT in the backend.

  TypeScript

  •

  MIT License

  •48•0•0•0•Updated Oct 16, 2024Oct 16, 2024

• hum-exomiser-fork

  Public
  A Tool to Annotate and Prioritize Exome Variants

  Java

  •

  GNU Affero General Public License v3.0

  •55•1•0•0•Updated Sep 20, 2024Sep 20, 2024

• hum-ngs-vntyper

  Public
  A tool to genotype MUC1 coding VNTR in ADTKD

  Python

  •3•0•0•0•Updated May 31, 2024May 31, 2024

• LB-tbdb

  Public
  Standard database for the TBProfiler tool

  Python

  •

  GNU Lesser General Public License v3.0

  •18•0•0•0•Updated May 13, 2024May 13, 2024

• ont-assembly-snake

  Public
  Snakemake workflow for bacterial genome assembly + polishing for Oxford Nanopore (ONT) sequencing using multiple tools.

  Python

  •

  MIT License

  •2•18•0•0•Updated Apr 23, 2024Apr 23, 2024

• score-assemblies

  Public
  Snakemake workflow for scoring and comparing multiple bacterial genome assemblies (Illumina, Nanopore) to reference genome(s).

  bioinformaticsgenome-analysisgenome-assembly+ 4nanopore-sequencingsnakemake-pipelinebacterial-genome-analysisnanopore-assembly

  Python

  •

  MIT License

  •1•24•0•0•Updated Apr 5, 2024Apr 5, 2024

• hum-cubi-tk-fork

  Public
  CUBI Tooling for SODAR, VarFish et al.

  Python

  •

  MIT License

  •6•0•0•1•Updated Mar 20, 2024Mar 20, 2024

• hum-varfish-annotator-fork

  Public
  Annotate variants for import into VarFish server.

  Java

  •

  MIT License

  •3•0•0•0•Updated Dec 1, 2023Dec 1, 2023

• hum-varfish-docker-compose-fork

  Public
  Setup VarFish as using Docker Compose

  Makefile

  •

  MIT License

  •3•0•0•0•Updated Dec 1, 2023Dec 1, 2023

• hum-varfish-server-fork

  Public
  VarFish: comprehensive DNA variant analysis for diagnostics and research

  Python

  •

  MIT License

  •11•0•0•0•Updated Dec 1, 2023Dec 1, 2023

• hum-varfish-db-downloader-fork

  Public
  Download public/static databases for VarFish

  Python

  •

  MIT License

  •3•0•0•0•Updated Dec 1, 2023Dec 1, 2023

• hum-varfish-cli-fork

  Public
  VarFish REST API client (CLI + Python package)

  Python

  •

  MIT License

  •3•0•0•0•Updated Dec 1, 2023Dec 1, 2023

• MultiQC

  Public
  Aggregate results from bioinformatics analyses across many samples into a single report.

  Python

  •

  GNU General Public License v3.0

  •601•1•1•0•Updated Oct 26, 2023Oct 26, 2023

• hum-gene-ranking-shootout

  Public
  A small benchmark for comparing gene ranking methods

  Python

  •

  MIT License

  •1•0•0•0•Updated May 11, 2023May 11, 2023

• bioconda-recipes

  Public
  Conda recipes for the bioconda channel.

  Shell

  •

  MIT License

  •3.3k•0•0•0•Updated Apr 5, 2023Apr 5, 2023

• MultiQC_TestData

  Public
  Test data for MultiQC. See https://github.com/ewels/MultiQC

  HTML

  •

  MIT License

  •144•0•0•0•Updated Mar 15, 2023Mar 15, 2023

• scramble

  Public
  R

  •

  Other

  •12•0•0•0•Updated Apr 5, 2022Apr 5, 2022

• LB-ncov2019-artic-nf

  Public
  A Nextflow pipeline for running the ARTIC network's fieldbioinformatics tools (https://github.com/artic-network/fieldbioinformatics), with a focus on ncov2019

  Nextflow

  •

  GNU Affero General Public License v3.0

  •88•1•0•0•Updated Mar 14, 2022Mar 14, 2022

• TBProfiler

  Public
  Profiling tool for Mycobacterium tuberculosis to detect ressistance and strain type from WGS data

  Python

  •

  GNU General Public License v3.0

  •43•0•0•0•Updated Nov 24, 2021Nov 24, 2021