CDCgov / MicrobeTraceLinks
The Visualization Multitool for Molecular Epidemiology and Bioinformatics
☆95Updated this week
Alternatives and similar repositories for MicrobeTrace
Users that are interested in MicrobeTrace are comparing it to the libraries listed below
Sorting:
- Reconstruction of transmission trees using genomic data☆71Updated 2 years ago
- R package for studying phylogenetically-informed movements (Dellicour et al. 2016, Bioinformatics; Dellicour et al., submitted)☆37Updated last week
- 🧬 💻 TOSTADAS → Toolkit for Open Sequence Triage, Annotation and DAtabase Submission☆28Updated 3 months ago
- Phylogenetics between and within hosts at once, all along the genome.☆50Updated last year
- Benchmark datasets for WGS analysis of SARS-CoV-2. (https://peerj.com/articles/13821/)☆58Updated 2 years ago
- Cluster Investigation & Virus Epidemiology Tool☆50Updated 6 months ago
- Global phylogenies of SARS-CoV-2 sequences☆85Updated 2 years ago
- Spatial Phylogenetic Reconstruction of Evolutionary Dynamics 3☆16Updated 2 years ago
- Rapid analysis and visualization of coronavirus genome variation☆48Updated this week
- Bioinformatics Pipeline and Visualization resources☆60Updated last year
- 🔥🐦🔥PHoeNIx: a platform agnostic pipeline for healthcare-associated and antimicrobial resistant pathogens☆89Updated this week
- An open database of vertebrate-virus interactions☆41Updated 3 weeks ago
- ☆74Updated last year
- Amplicon sequence processing workflow using QIIME 2 and Snakemake☆46Updated 3 weeks ago
- Programmatically interact with the GISAID database.☆80Updated 5 months ago
- Ultrafast Sample Placement on Existing Trees☆138Updated 3 weeks ago
- Collection template and associated materials for SARS-CoV-2 metadata☆37Updated 2 years ago
- MIRA: Portable, Interactive Application for High-Quality Influenza, SARS-CoV-2 and RSV Genome Assembly, Annotation, and Curation☆22Updated 3 months ago
- Prepares a SARS-CoV-2 submission for GISAID, NCBI or ENA. Can read GISAID or NCBI files, or plain fasta+tsv/csv/xls. Finds files in input…☆36Updated 3 years ago
- Small collection of tools for performing quality control on coronavirus sequencing data and genomes☆49Updated last year
- ☆50Updated 3 years ago
- Repository containing lists of all published ancient metagenomic (and related) samples and libraries☆77Updated last week
- Automated Pipeline to Generate FTP Files and Manage Submission of Sequence Data to Public Repositories☆38Updated this week
- This RAPT repository has been retired as of December 2024. NCBI's Read assembly and Annotation Pipeline Tool (RAPT) was a pilot service.☆58Updated 9 months ago
- A fast approximation to a Dirichlet Process Mixture model (DPM) for clustering genetic data☆68Updated 3 years ago
- Course materials for the Genomics Aotearoa Metagenomics Summer School, to be hosted at the University of Auckland in Septermber☆66Updated last year
- Genome wide orthology inference and dNdS estimation☆96Updated 4 months ago
- AMPtk: Amplicon ToolKit for NGS data (formally UFITS)☆39Updated 2 years ago
- A public repository for collective curation of antimicrobial resistance (AMR) genes and mutations. Submit, discuss, and resolve AMR curat…☆63Updated 3 months ago
- Viral Annotation DefineR: classification and annotation of viral sequences based on RefSeq annotation☆114Updated this week