rneher

rneher's Stars

• pcm-dpc/COVID-19

  COVID-19 Italia - Monitoraggio situazione

  3.9k2001.1k2.2k

• snakemake/snakemake

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

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• bbuchfink/diamond

  Accelerated BLAST compatible local sequence aligner.

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• globalcitizen/2019-wuhan-coronavirus-data

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

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• rrwick/Unicycler

  hybrid assembly pipeline for bacterial genomes

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• nextstrain/augur

  Pipeline components for real-time phylodynamic analysis

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• neherlab/treetime

  Maximum likelihood inference of time stamped phylogenies and ancestral reconstruction

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• nextstrain/nextclade

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

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• neherlab/pangraph

  A bioinformatic toolkit to align genome assemblies into pangenome graphs

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• blab/nextflu

  Real-time tracking of influenza evolution

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• robert-koch-institut/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.

  7511376

• neherlab/pan-genome-visualization

  Visualization of the pan-genome output by panX

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• cceh/suffix-tree

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

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• nextstrain/mpox

  Nextstrain build for mpox virus

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• INSaFLU/INSaFLU

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

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• nextstrain/nextclade_data

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

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• jbloomlab/SARS2-mut-fitness

  Observed substitution counts of SARS-CoV-2 compared to those expected under the mutation rates

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• iosonofabio/seqanpy

  Fast pairwise sequence alignment using SeqAn, in Python.

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• neherlab/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.

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• liampshaw/mobile-gene-regions

  Analysing the genomic context of mobile genes

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• mmolari/pypangraph

  Python package to manipulate pangenome graphs generated by PanGraph

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• iosonofabio/pysang

  A Sanger chromatograph viewer.

  Language:Python4202

• neherlab/HIV_fitness_landscape

  Analysis of fitness landscape of HIV-1 from longitudinal data

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• iosonofabio/hivwholeweb

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

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