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Richard Neher (rneher)

rneher

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Company:Biozentrum, University of Basel

Location:Basel, Switzerland

Home Page:https://mstdn.science/@richardneher

Twitter:@richardneher

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neherlab
nextstrain

Richard Neher's starred repositories

COVID-19

COVID-19 Italia - Monitoraggio situazione

License:NOASSERTIONStargazers:3877Issues:200Issues:1086

snakemake

This is the development home of the workflow management system Snakemake. For general information, see

Language:HTMLLicense:MITStargazers:2182Issues:19Issues:1633

diamond

Accelerated BLAST compatible local sequence aligner.

Language:C++License:GPL-3.0Stargazers:994Issues:36Issues:685

2019-wuhan-coronavirus-data

2019 Wuhan Coronavirus data (COVID-19 / 2019-nCoV)

Language:PHPLicense:GPL-3.0Stargazers:616Issues:62Issues:0

Unicycler

hybrid assembly pipeline for bacterial genomes

Language:C++License:GPL-3.0Stargazers:536Issues:30Issues:323

augur

Pipeline components for real-time phylodynamic analysis

Language:PythonLicense:AGPL-3.0Stargazers:268Issues:31Issues:633

treetime

Maximum likelihood inference of time stamped phylogenies and ancestral reconstruction

Language:Jupyter NotebookLicense:MITStargazers:214Issues:17Issues:141

nextclade

Viral genome alignment, mutation calling, clade assignment, quality checks and phylogenetic placement

Language:RustLicense:MITStargazers:204Issues:19Issues:442

nextflu

Real-time tracking of influenza evolution

Language:JavaScriptLicense:AGPL-3.0Stargazers:86Issues:29Issues:74

pangraph

A bioinformatic toolkit to align genome assemblies into pangenome graphs

Language:JuliaLicense:MITStargazers:77Issues:8Issues:22

SARS-CoV-2-Infektionen_in_Deutschland_Archiv

Der vorliegende Datansatz enthält umfassende Informationen zu SARS-CoV-2-Infektionen in Deutschland, die gemäß dem Infektionsschutzgesetze (IfSG) von den Gesundheitsämtern an das Robert Koch-Institut (RKI) gemeldet wurden. Die Daten umfassen Informationen zur Anzahl der bestätigten Fälle, Todesfälle und Genesungen.

License:CC-BY-4.0Stargazers:75Issues:12Issues:37

pan-genome-visualization

Visualization of the pan-genome output by panX

Language:JavaScriptLicense:NOASSERTIONStargazers:59Issues:9Issues:14

mpox

Nextstrain build for mpox virus

Language:PythonLicense:MITStargazers:39Issues:17Issues:44

suffix-tree

A Generalized Suffix Tree for any Python iterable using Ukkonen's algorithm, with Lowest Common Ancestor retrieval.

Language:PythonLicense:GPL-3.0Stargazers:38Issues:9Issues:5

INSaFLU

INSaFLU-TELEVIR: an free web-based (but also locally installable) bioinformatics suite for virus metagenomic detection and routine genomic surveillance

Language:PythonLicense:GPL-3.0Stargazers:29Issues:6Issues:5

nextclade_data

Datasets for https://github.com/nextstrain/nextclade

Language:PythonStargazers:28Issues:12Issues:34

seqanpy

Fast pairwise sequence alignment using SeqAn, in Python.

Language:C++License:NOASSERTIONStargazers:13Issues:4Issues:1

ffpopsim

FFPopSim is a collection of C++ classes and a Python interface for efficient simulation of large populations, in particular when the product of mutation rate and population size is larger than one. It consists of one library for individual-based simulations, and a complementary one for simulation of the entire genotype distribution. The latter is coded efficiently using Fast-Fourier Transforms to speed up recombination operations.

Language:C++License:GPL-3.0Stargazers:13Issues:7Issues:3

pysang

A Sanger chromatograph viewer.

Language:PythonStargazers:4Issues:2Issues:0

hivwholeweb

Web application for deep sequencing on longitudinal HIV-1 samples from patients.

Language:JavaScriptLicense:NOASSERTIONStargazers:3Issues:4Issues:2

HIV_fitness_landscape

Analysis of fitness landscape of HIV-1 from longitudinal data

Language:PythonStargazers:3Issues:1Issues:0