Repositories list

• ont-methylation

  Public
  Nextflow

  •

  GNU General Public License v3.0

  •0•2•4•0•Updated Mar 20, 2025Mar 20, 2025

• viruswarn-sc2

  Public
  VirusWarn-SC2 is a simple Variants of concern aLert system script for Sars-CoV2. Doc https://rki-mf1.github.io/vocal-doc/

  vocalvariant-detectionsars-cov-2+ 2early-warning-systemintegrated-molecular-surveillance

  HTML

  •

  MIT License

  •1•5•6•0•Updated Mar 5, 2025Mar 5, 2025

• VirusWarn-Flu

  Public
  A mutation-based alert system to prioritize concerning Influenza variants from sequencing data.

  influenzaearly-warning-systemsvariant-detection+ 1integrated-molecular-surveillance

  HTML

  •

  MIT License

  •0•0•0•0•Updated Mar 5, 2025Mar 5, 2025

• FluPipe

  Public
  Influenza genome reconstruction

  Python

  •

  GNU General Public License v3.0

  •1•5•1•0•Updated Feb 27, 2025Feb 27, 2025

• update-varvamp-bed

  Public
  to update the primer bed positions from varvamp results based on given reference

  Python

  •0•1•1•0•Updated Feb 24, 2025Feb 24, 2025

• bx_pip_medaka

  Public
  Dockerfile

  •0•0•0•0•Updated Feb 21, 2025Feb 21, 2025

• bx_medaka

  Public
  Dockerfile

  •0•0•0•0•Updated Feb 20, 2025Feb 20, 2025

• GARI

  Public
  Nextflow

  •

  MIT License

  •0•0•1•0•Updated Feb 7, 2025Feb 7, 2025

• AMRFlow

  Public
  AMRFlow - a Nextflow-based pipeline designed for the integrated genomic surveillance of pathogens, enhancing antimicrobial resistance detection through customizable, multi-tool analyses

  Nextflow

  •

  MIT License

  •0•0•2•0•Updated Feb 5, 2025Feb 5, 2025

• CoVpipe2

  Public
  SARS-CoV-2 genome reconstruction for Illumina data in Nextflow

  Nextflow

  •

  GNU General Public License v3.0

  •1•4•12•0•Updated Jan 20, 2025Jan 20, 2025

• PanAdapt

  Public
  Jupyter Notebook

  •0•0•3•0•Updated Jan 8, 2025Jan 8, 2025

• clean

  Public
  A nextflow pipeline for decontamination of short reads, long reads and contigs

  Nextflow

  •

  BSD 3-Clause "New" or "Revised" License

  •5•44•7•0•Updated Dec 19, 2024Dec 19, 2024

• breakfast

  Public
  breakfast is a simple and fast tool for clustering SARS-CoV-2 genomes using precalculated sequence features (e.g. nucleotide substitutions).

  bioinformaticsclustering

  Python

  •

  MIT License

  •1•10•7•0•Updated Nov 15, 2024Nov 15, 2024

• covsonar

  Public
  A database-driven system for handling genomic sequences of SARS-CoV-2 and screening genomic profiles.

  bioinformaticsdatabasesars-cov-2+ 2covsonargenomic-profiles

  Python

  •

  GNU General Public License v3.0

  •0•6•6•2•Updated Nov 4, 2024Nov 4, 2024

• 2024-SC2-Data-Science

  Public
  Material for the SARS-CoV-2 data science course at FU Berlin.

  Shell

  •

  GNU General Public License v3.0

  •14•1•0•0•Updated Sep 30, 2024Sep 30, 2024

• sc2-mutation-frequency-calculator

  Public
  Python tool to calculate characteristic and signature mutations based on mutation profiles for a certain timeframe.

  Python

  •0•0•3•0•Updated Sep 27, 2024Sep 27, 2024

• cievad

  Public
  A tool suite for a simple, streamlined and rapid evaluation of variant callsets

  benchmarkingbioinformaticssnps+ 6genomicsnextflowngsvariant-callingoxford-nanoporeindels

  Nextflow

  •

  GNU General Public License v3.0

  •1•6•7•0•Updated Sep 16, 2024Sep 16, 2024

• VLQ-nf

  Public
  Estimate SC2 lineage abundances from wastewater samples

  Nextflow

  •

  GNU General Public License v3.0

  •0•3•3•0•Updated Aug 6, 2024Aug 6, 2024

• covsonar2

  Public
  covsonar 2: an updated version of covsonar, our database for storing and querying mutations and metadata

  Python

  •

  GNU General Public License v3.0

  •0•0•1•2•Updated Jul 15, 2024Jul 15, 2024

• 2024-Workshop-EEBG

  Public
  Eastern European Bioinformatics and Computational Genomics School (EEBG): Primer on linux, nanopore, and metagenomics

  Shell

  •

  GNU General Public License v3.0

  •14•3•0•0•Updated Jul 12, 2024Jul 12, 2024

• workshop-nanopore-bioinformatics

  Public
  Main resource for practical introductions to long-read bioinformatics.

  Shell

  •

  GNU General Public License v3.0

  •14•2•13•0•Updated Jun 30, 2024Jun 30, 2024

• modules

  Public
  Repository to host tool-specific module files for the Nextflow DSL2 community!

  Nextflow

  •

  MIT License

  •785•0•0•0•Updated Apr 3, 2024Apr 3, 2024

• 2024-Workshop-Namibia

  Public
  Practical introduction to long-read bioinformatics on the flu virus .

  Shell

  •

  GNU General Public License v3.0

  •14•2•0•0•Updated Mar 15, 2024Mar 15, 2024

• amplisim

  Public
  Plain simple amplicon sequence simulator for in-silico genomic sequencing assays

  C++

  •

  Apache License 2.0

  •0•2•7•0•Updated Mar 7, 2024Mar 7, 2024

• MpoxRadar

  Public
  MpoxRadar frontend codebase: an interactive dashboard for genomic surveillance of MPXV.

  dashboardfrontendhpi+ 3rkigenomic-surveillancempox

  Python

  •

  GNU General Public License v3.0

  •1•3•1•0•Updated Dec 2, 2023Dec 2, 2023

• 2023-Workshop-Madagascar-IGS

  Public
  A practical introduction to short-read bioinformatics for bacterial genome reconstruction in the context of the Madagascar IGS workshop.ct.

  Shell

  •

  GNU General Public License v3.0

  •14•1•0•0•Updated Oct 12, 2023Oct 12, 2023

• 2023-GHPP-SGS-Nanopore-Metagenomics

  Public
  A practical introduction to long-read metagenomics in the context of the 2023 GHPP "Strengthening Genomic Surveillance" workshop..

  Shell

  •

  GNU General Public License v3.0

  •14•2•4•0•Updated Sep 27, 2023Sep 27, 2023

• MpoxSonar

  Public
  Python

  •

  GNU General Public License v3.0

  •0•2•0•0•Updated Sep 27, 2023Sep 27, 2023

• 2023-SC2-Data-Science

  Public
  Material for the SARS-CoV-2 data science course at FU Berlin.

  Shell

  •

  GNU General Public License v3.0

  •14•3•0•0•Updated Sep 21, 2023Sep 21, 2023

• 2023-NGS-Summer-School

  Public
  NGS Summer School about Nanopore long-read bioinformatics and bacteria genome assembly.

  Shell

  •

  GNU General Public License v3.0

  •14•0•0•0•Updated Aug 30, 2023Aug 30, 2023