CDCgov / MicrobeTraceLinks
The Visualization Multitool for Molecular Epidemiology and Bioinformatics
☆94Updated 2 weeks ago
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☆63Updated last year
- Benchmark datasets for WGS analysis of SARS-CoV-2. (https://peerj.com/articles/13821/)☆56Updated 2 years ago
- R package for studying phylogenetically-informed movements (Dellicour et al. 2016, Bioinformatics; Dellicour et al., in prep.)☆34Updated last week
- 🧬 💻 TOSTADAS → Toolkit for Open Sequence Triage, Annotation and DAtabase Submission☆28Updated this week
- Global phylogenies of SARS-CoV-2 sequences☆86Updated last year
- Cluster Investigation & Virus Epidemiology Tool☆50Updated 2 months ago
- Phylogenetics between and within hosts at once, all along the genome.☆50Updated 11 months ago
- Rapid analysis and visualization of coronavirus genome variation☆48Updated last month
- Collection template and associated materials for SARS-CoV-2 metadata☆35Updated last year
- An open database of vertebrate-virus interactions☆41Updated last week
- 🔥🐦🔥PHoeNIx: a platform agnostic pipeline for healthcare-associated and antimicrobial resistant pathogens☆83Updated this week
- Programmatically interact with the GISAID database.☆78Updated last month
- ☆74Updated last year
- Amplicon sequence processing workflow using QIIME 2 and Snakemake☆47Updated this week
- MIRA: Portable, Interactive Application for High-Quality Influenza, SARS-CoV-2 and RSV Genome Assembly, Annotation, and Curation☆19Updated 2 weeks ago
- Bioinformatics Pipeline and Visualization resources☆57Updated last year
- SHallow shOtGUN profiler☆54Updated 3 years ago
- Identify Variants of Concern from metagenomic samples of SARS-CoV-2☆13Updated 3 years ago
- ☆49Updated 3 years ago
- Spatial Phylogenetic Reconstruction of Evolutionary Dynamics 3☆16Updated 2 years ago
- Simple R utilities for working with HMMER☆20Updated 11 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
- Source files for online resources of Bioinformatics of Infectious Diseases course☆22Updated 5 years ago
- A visualization tool for exploratory data analysis of metagenomic data☆37Updated 3 years ago
- AMPtk: Amplicon ToolKit for NGS data (formally UFITS)☆38Updated last year
- Automated Pipeline to Generate FTP Files and Manage Submission of Sequence Data to Public Repositories☆38Updated last week
- Bioinformatics workflows for genomic characterization, submission preparation, and genomic epidemiology of pathogens of public health con…☆55Updated last week
- Snakemake-based amplicon processing protocol for 16S and ITS sequences.☆14Updated last year
- A tool for exploring large trees in the browser☆114Updated last week
- Consensus sequences for U.S. H5N1 clade 2.3.4.4b☆36Updated last week