nextstrain / augurLinks
Pipeline components for real-time phylodynamic analysis
☆271Updated last week
Alternatives and similar repositories for augur
Users that are interested in augur are comparing it to the libraries listed below
Sorting:
- Viral genome alignment, mutation calling, clade assignment, quality checks and phylogenetic placement☆242Updated this week
- Quickly search, compare, and analyze genomic and metagenomic data sets.☆517Updated this week
- Web app for visualizing pathogen evolution☆302Updated last week
- An analysis and visualization platform for 'omics data☆480Updated this week
- PhyML -- Phylogenetic estimation using (Maximum) Likelihood☆188Updated 3 weeks ago
- Maximum likelihood inference of time stamped phylogenies and ancestral reconstruction☆242Updated this week
- A collection of sequencing protocols and bioinformatic resources for SARS-CoV-2 sequencing.☆348Updated 2 years ago
- HyPhy: Hypothesis testing using Phylogenies☆237Updated 3 weeks ago
- Ongoing analysis of COVID-19 using Galaxy, BioConda and public research infrastructures☆128Updated 2 years ago
- AMRFinderPlus - Identify AMR genes and point mutations, and virulence and stress resistance genes in assembled bacterial nucleotide and p…☆319Updated 3 weeks ago
- ☆115Updated 2 years ago
- Ultra-deep search for novel viruses☆272Updated 2 years ago
- Tool Shed repositories maintained by the Intergalactic Utilities Commission☆182Updated this week
- Artemis is a free genome viewer and annotation tool that allows visualization of sequence features and the results of analyses within the…☆250Updated last year
- Viral Annotation DefineR: classification and annotation of viral sequences based on RefSeq annotation☆110Updated last month
- [MOVED] Moved to paoloshasta/shasta. De novo assembly from Oxford Nanopore reads☆274Updated 2 years ago
- Nanopore sequence read simulator☆276Updated 5 months ago
- An updated pipeline for pangenome investigation☆308Updated 5 months ago
- ATLAS - Three commands to start analyzing your metagenome data☆394Updated 3 months ago
- Antimicrobial Resistance Identification By Assembly☆179Updated last year
- Infectious Disease Sequencing Platform☆87Updated 2 weeks ago
- Profiling tool for Mycobacterium tuberculosis to detect ressistance and strain type from WGS data☆120Updated last week
- Assemble large genomes using short reads☆322Updated 4 months ago
- [THIS REPO IS DEPRECATED] see newer repos: https://github.com/broadinstitute/viral-core https://github.com/broadinstitute/viral-assemble …☆195Updated 10 months ago
- baltic - backronymed adaptable lightweight tree import code for molecular phylogeny manipulation, analysis and visualisation. Development…☆107Updated last week
- Build a partitioned pangenome graph from microbial genomes☆275Updated last week
- A Python library for phylogenetic scripting, simulation, data processing and manipulation.☆218Updated last month
- Scripts. config, and snakefiles for seasonal-flu nextstrain builds☆50Updated this week
- Fast genome and metagenome distance estimation using MinHash☆417Updated last year
- Utilities for building and managing bioconda recipes☆103Updated this week