CDCgov / MicrobeTrace
The Visualization Multitool for Molecular Epidemiology and Bioinformatics
β88Updated last month
Related projects β
Alternatives and complementary repositories for MicrobeTrace
- 𧬠π» TOSTADAS β Toolkit for Open Sequence Triage, Annotation and DAtabase Submissionβ27Updated this week
- Benchmark datasets for WGS analysis of SARS-CoV-2. (https://peerj.com/articles/13821/)β54Updated last year
- R package for studying environmental rasters and phylogenetic informed movements (Dellicour et al. 2016, Bioinformatics; Dellicour et al.β¦β29Updated 3 weeks ago
- Cluster Investigation & Virus Epidemiology Toolβ49Updated last year
- Phylogenetics between and within hosts at once, all along the genome.β47Updated last month
- Reconstruction of transmission trees using genomic dataβ60Updated last year
- β14Updated 2 weeks ago
- Bioinformatics Pipeline and Visualization resourcesβ54Updated 2 months ago
- Automated Pipeline to Generate FTP Files and Manage Submission of Sequence Data to Public Repositoriesβ32Updated this week
- CZID (formerly IDseq) infectious disease command-line interfaceβ21Updated 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 inputβ¦β35Updated 2 years ago
- Spatial Phylogenetic Reconstruction of Evolutionary Dynamics 3β13Updated last year
- π₯π¦π₯PHoeNIx: A short-read pipeline for healthcare-associated and antimicrobial resistant pathogensβ59Updated this week
- β48Updated 2 years ago
- Viral Annotation DefineR: classification and annotation of viral sequences based on RefSeq annotationβ99Updated 3 months ago
- Tutorial on using E-utilitiesβ19Updated 3 years ago
- Global phylogenies of SARS-CoV-2 sequencesβ86Updated last year
- Programmatically interact with the GISAID database.β72Updated 2 months ago
- serious constellations of reoccurring phylogenetically-independent originβ38Updated last year
- Schloss Lab Tools for Reproducible Microbiome Research π©β29Updated last year
- A comprehensive pipeline for short read metagenomic dataβ24Updated 4 years ago
- A visualization tool for exploratory data analysis of metagenomic dataβ36Updated 2 years ago
- A library and collection of scripts to work with Illumina paired-end data (for CASAVA 1.7+ pipeline).β91Updated 11 months ago
- A set of R scripts for the analysis of microbial profilesβ40Updated 6 months ago
- An open database of vertebrate-virus interactionsβ37Updated 3 weeks ago
- Harmonization of AMR predictor tool outputsβ21Updated last year
- QIIME 2 plugin wrapping DADA2β19Updated 3 weeks ago
- Basestack is a platform for rapid and real time analysis of NGS data. It provides a executable application that connects standard bionforβ¦β26Updated 3 months ago
- Rapid analysis and visualization of coronavirus genome variationβ46Updated this week
- Parse NCBI taxonomy and accessions to find taxonomic assignmentsβ70Updated 11 months ago