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@rki-mf1 RKI MF1 Bioinformatics

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    55 repositories

    • breakfast

      Public
      breakfast is a simple and fast tool for clustering SARS-CoV-2 genomes using precalculated sequence features (e.g. nucleotide substitutions).
      bioinformaticsclustering
      bioinformaticsclustering
      Python
      •
      MIT License
      •1•11•8•1•Updated Mar 12, 2026Mar 12, 2026

    • sonar

      Public
      Centrally store and search large amounts of genomic mutations and metadata.
      Python
      •
      Other
      •0•1•77•6•Updated Mar 7, 2026Mar 7, 2026

    • hiv_subtyping

      Public
      Python
      •1•0•0•0•Updated Mar 6, 2026Mar 6, 2026

    • omnifluss_downstream

      Public
      Omnifluss pipeline for downstream analyses
      Nextflow
      •
      MIT License
      •0•0•2•0•Updated Mar 2, 2026Mar 2, 2026

    • mgwatch

      Public
      MetagenomeWatch
      Python
      •
      GNU Affero General Public License v3.0
      •1•6•37•1•Updated Feb 24, 2026Feb 24, 2026

    • ont-qc

      Public
      Nextflow pipeline for ONT QC including filtering and preliminary taxonomic classification
      Nextflow
      •1•1•0•0•Updated Feb 19, 2026Feb 19, 2026

    • GARI

      Public
      Nextflow
      •
      MIT License
      •0•1•1•0•Updated Jan 26, 2026Jan 26, 2026

    • 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•4•Updated Jan 16, 2026Jan 16, 2026

    • inv-update-segment-db

      Public
      Update pipeline for the reference segment DB for FluPipe (https://github.com/rki-mf1/FluPipe)
      Nextflow
      •
      MIT License
      •0•1•2•0•Updated Dec 17, 2025Dec 17, 2025

    • sc2-mutation-frequency-calculator

      Public
      Python tool to calculate characteristic and signature mutations based on mutation profiles for a certain timeframe.
      Python
      •0•1•4•0•Updated Dec 17, 2025Dec 17, 2025

    • crymco

      Public
      Detection of cryptic mutation profiles in SARS-CoV-2 metagenomes through variant co-occurrence
      Python
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Dec 12, 2025Dec 12, 2025

    • omnifluss

      Public
      Computational workflow for virus genome reconstruction
      virusnextflownf-core
      virusnextflownf-coregenome-reconstruction
      Nextflow
      •
      MIT License
      •0•9•11•1•Updated Dec 11, 2025Dec 11, 2025

    • LARRI

      Public
      Long-reads Assembly Reconstruction and Refinement pIpeline - bacterial assembly from long reads
      Nextflow
      •
      GNU General Public License v3.0
      •0•1•5•0•Updated Dec 5, 2025Dec 5, 2025

    • ont-methylation

      Public
      Nextflow
      •
      GNU General Public License v3.0
      •0•17•3•0•Updated Dec 4, 2025Dec 4, 2025

    • cgps-mlst-flow

      Public
      CGPS-MLST-Flow is a Nextflow wrapper for CGPS (cg)MLST.
      R
      •
      MIT License
      •0•0•0•0•Updated Nov 19, 2025Nov 19, 2025

    • btr-omakub

      Public
      Opinionated Ubuntu Setup for BTR
      Shell
      •794•0•4•0•Updated Nov 5, 2025Nov 5, 2025

    • hiv_tsi

      Public
      Estimation of Time since Infection for HIV Samples
      Python
      •1•0•0•0•Updated Nov 4, 2025Nov 4, 2025

    • omnifluss_data

      Public
      Test data repository for the Omnifluss virus genome reconstruction pipeline
      0•0•0•0•Updated Oct 23, 2025Oct 23, 2025

    • viruswarn-sc2

      Public
      VirusWarn-SC2 is a simple Variants of concern aLert system script for SARS-CoV-2.
      vocalvariant-detectionsars-cov-2
      vocalvariant-detectionsars-cov-2early-warning-systemintegrated-molecular-surveillance
      HTML
      •
      MIT License
      •1•7•1•0•Updated Oct 10, 2025Oct 10, 2025

    • 2025-SC2-Data-Science

      Public
      Material for the SARS-CoV-2 data science course at FU Berlin.
      Shell
      •
      GNU General Public License v3.0
      •16•2•0•0•Updated Oct 1, 2025Oct 1, 2025

    • anobac

      Public
      Bacterial annotation and typing pipeline
      R
      •
      MIT License
      •0•1•0•0•Updated Sep 2, 2025Sep 2, 2025

    • AMRFlow

      Public
      AMRFlow - a Nextflow-based pipeline designed for the integrated genomic surveillance of pathogens, enhancing antimicrobial resistance detection through customiz…
      Nextflow
      •
      MIT License
      •1•2•2•0•Updated Sep 2, 2025Sep 2, 2025

    • bx_dorado_basecaller

      Public
      Dockerfile
      •0•0•0•0•Updated Aug 25, 2025Aug 25, 2025

    • bx_modkit

      Public
      docker container for modkit 0.5.0
      Dockerfile
      •0•0•0•0•Updated Aug 25, 2025Aug 25, 2025

    • clean

      Public
      A nextflow pipeline for decontamination of short reads, long reads and contigs
      Nextflow
      •
      BSD 3-Clause "New" or "Revised" License
      •5•54•8•0•Updated Jun 30, 2025Jun 30, 2025

    • VirusWarn-Flu

      Public
      A mutation-based alert system to prioritize concerning Influenza variants from sequencing data.
      influenzaearly-warning-systemsvariant-detection
      influenzaearly-warning-systemsvariant-detectionintegrated-molecular-surveillance
      HTML
      •
      MIT License
      •0•2•0•0•Updated Mar 5, 2025Mar 5, 2025

    • FluPipe

      Public
      Influenza genome reconstruction
      Python
      •
      GNU General Public License v3.0
      •1•6•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•2•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