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2023-ghpp-sgs-nanopore-metagenomics

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

2023-ngs-summer-school

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

2023-sc2-data-science

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

2023-workshop-madagascar-igs

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

2023-workshop-mission-nanopore

A practical introduction to long-read bioinformatics for bacterial genome reconstruction in the context of the Kenya MISSIoN project.

2024-workshop-eebg

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

2024-workshop-namibia

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

amplisim

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

breakfast

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

cievad

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

clean

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

coverageanomalyscanner

Application to find local anomalies in read coverage and to predict putative SV events

covpipe2

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

covsonar

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

covsonar2

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

find_giardia_primer_regions

Snakemake pipeline to find potential giardia primer regions

flupipe

Influenza genome reconstruction

lcs

modules

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

mpoxradar

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

mpoxsonar

panadapt

president

rki-mf1.github.io

RKI Bioinformatics Research team page

rubyscholar

Scrape Google Scholar Profile into a custom HTML using Ruby (Nokogiri)

sc2-mutation-frequency-calculator

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

update-varvamp-bed

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

vlq-nf

Estimate SC2 lineage abundances from wastewater samples

vocal

Vocal is a simple Variants Of Concern ALert system script. Doc https://rki-mf1.github.io/vocal-doc/

workshop-nanopore-bioinformatics

Main resource for practical introductions to long-read bioinformatics.