RKI MF1 Bioinformatics (rki-mf1)

RKI MF1 Bioinformatics

rki-mf1

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Bioinformatics code of MF1

Location:Germany

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RKI MF1 Bioinformatics's repositories

clean

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

Language:NextflowLicense:BSD-3-ClauseStargazers:27Issues:6Issues:47

breakfast

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

Language:PythonLicense:MITStargazers:10Issues:4Issues:8

covsonar

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

Language:PythonLicense:GPL-3.0Stargazers:6Issues:5Issues:79

vocal

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

2023-SC2-Data-Science

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

Language:ShellLicense:GPL-3.0Stargazers:4Issues:0Issues:0

2024-Workshop-EEBG

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

Language:ShellLicense:GPL-3.0Stargazers:3Issues:0Issues:0

FluPipe

Influenza genome reconstruction

Language:PythonLicense:GPL-3.0Stargazers:3Issues:3Issues:1

2023-GHPP-SGS-Nanopore-Metagenomics

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

Language:ShellLicense:GPL-3.0Stargazers:2Issues:0Issues:0

2023-Workshop-MISSIoN-Nanopore

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

Language:ShellLicense:GPL-3.0Stargazers:2Issues:3Issues:10

2024-Workshop-Namibia

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

Language:ShellLicense:GPL-3.0Stargazers:2Issues:0Issues:0

amplisim

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

Language:C++License:Apache-2.0Stargazers:2Issues:1Issues:8

cievad

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

Language:NextflowLicense:GPL-3.0Stargazers:2Issues:0Issues:0

CoVpipe2

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

Language:NextflowLicense:GPL-3.0Stargazers:2Issues:3Issues:29

MpoxRadar

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

Language:PythonLicense:GPL-3.0Stargazers:2Issues:5Issues:1
Language:PythonLicense:GPL-3.0Stargazers:2Issues:4Issues:0
Language:PythonLicense:MITStargazers:2Issues:3Issues:4

VLQ-nf

Estimate SC2 lineage abundances from wastewater samples

Language:NextflowLicense:GPL-3.0Stargazers:2Issues:2Issues:1

2023-Workshop-Madagascar-IGS

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

Language:ShellLicense:GPL-3.0Stargazers:1Issues:0Issues:0

update-varvamp-bed

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

Language:PythonStargazers:1Issues:0Issues:0

workshop-nanopore-bioinformatics

Main resource for practical introductions to long-read bioinformatics.

Language:ShellLicense:GPL-3.0Stargazers:1Issues:0Issues:0

2023-NGS-Summer-School

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

Language:ShellLicense:GPL-3.0Stargazers:0Issues:0Issues:0

CoverageAnomalyScanner

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

Language:C++License:GPL-3.0Stargazers:0Issues:0Issues:0
Language:Jupyter NotebookStargazers:0Issues:0Issues:0

rki-mf1.github.io

RKI Bioinformatics Research team page

Language:PythonLicense:GPL-3.0Stargazers:0Issues:0Issues:0

rubyscholar

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

Language:RubyLicense:MITStargazers:0Issues:0Issues:0

covsonar2

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

Language:PythonLicense:GPL-3.0Stargazers:0Issues:0Issues:0

Find_Giardia_Primer_Regions

Snakemake pipeline to find potential giardia primer regions

Language:PythonLicense:GPL-3.0Stargazers:0Issues:0Issues:0

modules

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

Language:NextflowLicense:MITStargazers:0Issues:0Issues:0
Language:Jupyter NotebookStargazers:0Issues:3Issues:6

sc2-mutation-frequency-calculator

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

Language:PythonStargazers:0Issues:0Issues:0