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@rki-mf1 RKI MF1 Bioinformatics

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    34 repositories

    • clean

      Public
      A nextflow pipeline for decontamination of short reads, long reads and contigs
      Nextflow
      •
      BSD 3-Clause "New" or "Revised" License
      •3•32•6•0•Updated Dec 19, 2024Dec 19, 2024

    • CoVpipe2

      Public
      SARS-CoV-2 genome reconstruction for Illumina data in Nextflow
      Nextflow
      •
      GNU General Public License v3.0
      •1•4•12•0•Updated Dec 19, 2024Dec 19, 2024

    • 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•0•0•Updated Dec 18, 2024Dec 18, 2024

    • GARI

      Public
      Nextflow
      •
      MIT License
      •0•0•3•1•Updated Dec 12, 2024Dec 12, 2024

    • FluPipe

      Public
      Influenza genome reconstruction
      Python
      •
      GNU General Public License v3.0
      •0•4•1•0•Updated Dec 2, 2024Dec 2, 2024

    • PanAdapt

      Public
      Jupyter Notebook
      •0•0•3•0•Updated Dec 2, 2024Dec 2, 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

    • VirusWarn-Flu

      Public
      A mutation-based alert system to prioritize concerning Influenza variants from sequencing data.
      influenzaearly-warning-systemsvariant-detectionintegrated-molecular-surveillance
      HTML
      •
      MIT License
      •0•0•0•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-2covsonargenomic-profiles
      Python
      •
      GNU General Public License v3.0
      •0•6•6•2•Updated Nov 4, 2024Nov 4, 2024

    • 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-2early-warning-systemintegrated-molecular-surveillance
      HTML
      •
      MIT License
      •1•5•6•0•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
      benchmarkingbioinformaticssnpsgenomicsnextflowngsvariant-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
      •735•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

    • update-varvamp-bed

      Public
      to update the primer bed positions from varvamp results based on given reference
      Python
      •0•1•0•0•Updated Feb 14, 2024Feb 14, 2024

    • MpoxRadar

      Public
      MpoxRadar frontend codebase: an interactive dashboard for genomic surveillance of MPXV.
      dashboardfrontendhpirkigenomic-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•4•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

    • 2023-Workshop-MISSIoN-Nanopore

      Public
      A practical introduction to long-read bioinformatics for bacterial genome reconstruction in the context of the Kenya MISSIoN project.
      Shell
      •
      GNU General Public License v3.0
      •14•2•0•0•Updated Aug 22, 2023Aug 22, 2023

    • Find_Giardia_Primer_Regions

      Public
      Snakemake pipeline to find potential giardia primer regions
      Python
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Jul 20, 2023Jul 20, 2023

    • CoverageAnomalyScanner

      Public
      Application to find local anomalies in read coverage and to predict putative SV events
      C++
      •
      GNU General Public License v3.0
      •0•0•2•0•Updated Feb 2, 2023Feb 2, 2023