The Visualization Multitool for Molecular Epidemiology and Bioinformatics
β98Updated this week
Alternatives and similar repositories for MicrobeTrace
Users that are interested in MicrobeTrace are comparing it to the libraries listed below
Sorting:
- 𧬠π» TOSTADAS β Toolkit for Open Sequence Triage, Annotation and DAtabase Submissionβ28Feb 19, 2026Updated last week
- Software for the Tree-Based Scan Statisticβ14Updated this week
- React component for visualizing your data on a map of the United States based off work done for the CDCβ10Dec 14, 2020Updated 5 years ago
- An SRA tool that takes as input local fastq file from a clinical infection sample, identifies and removes any significant human read, andβ¦β52Jul 24, 2025Updated 7 months ago
- Automated Pipeline to Generate FTP Files and Manage Submission of Sequence Data to Public Repositoriesβ38Feb 20, 2026Updated last week
- Main development repository for SpreadGLβ20Sep 30, 2024Updated last year
- Bioinformatics workflows for genomic characterization, submission preparation, and genomic epidemiology of viral pathogens of concern, esβ¦β42Aug 5, 2024Updated last year
- Fast, scalable, accurate and accessible Bayesian phylogeneticsβ42Feb 20, 2026Updated last week
- Official place for proposals and details around monkeypox virus lineage designationsβ23Dec 9, 2025Updated 2 months ago
- Static website for the PH4AGE allianceβ13Oct 27, 2023Updated 2 years ago
- Summarise nucleotide counts at a set of positions in a BAM file to search for mixturesβ13Apr 5, 2022Updated 3 years ago
- β27Aug 2, 2023Updated 2 years ago
- de novo virus assembler of Illumina paired readsβ58May 17, 2021Updated 4 years ago
- Bioinformatics workflows for genomic characterization, submission preparation, and genomic epidemiology of pathogens of public health conβ¦β61Updated this week
- 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¦β36May 1, 2022Updated 3 years ago
- β13Nov 1, 2022Updated 3 years ago
- A message queue for genomic surveillanceβ19Oct 14, 2021Updated 4 years ago
- A pipeline for preprocessing NGS data from Illumina, Nanopore and PacBio technologiesβ35Jun 30, 2024Updated last year
- Consensus sequences for U.S. H5N1 clade 2.3.4.4bβ37Updated this week
- Bioinformatics Pipeline and Visualization resourcesβ62Aug 30, 2024Updated last year
- An API, a query engine, and a database schema for genomic sequences; currently with a focus on SARS-CoV-2β29Updated this week
- Programmatically interact with the GISAID database.β80Aug 5, 2025Updated 6 months ago
- β30Mar 6, 2025Updated 11 months ago
- emm Automatic Isolate Labellerβ12Mar 25, 2025Updated 11 months ago
- SARS-CoV-2: detecting recombinations in viruses using large data sets with high sequence similarityβ13Aug 14, 2023Updated 2 years ago
- β20Apr 2, 2025Updated 10 months ago
- A Signature R package for the National Syndromic Surveillance Program (NSSP) at the Centers for Disease Control and Prevention (CDC). A cβ¦β46Nov 20, 2025Updated 3 months ago
- UPHL's Reference Free Pipelineβ27Updated this week
- Rapid determination of appropriate reference genomes.β100Jan 22, 2025Updated last year
- This is the repository for the openCDC web site. Entire site is generated from data files describing CDC Open Technology types for data, β¦β18Mar 21, 2024Updated last year
- Perl and Python scripts allowing to get sequence information from GenBank, RefSeq or ENA sequence repositoriesβ14Mar 29, 2025Updated 11 months ago
- A tool for exploring large trees in the browserβ123Feb 4, 2026Updated 3 weeks ago
- A methodology to rapidly leverage whole genome sequencing of bacterial isolates for clinical identification.β35Dec 2, 2024Updated last year
- Repository containing a method for automatically identifying pathogen lineages from a phylogeny.β17May 19, 2023Updated 2 years ago
- Sequence Indexing engine for Large Omics dataβ18Updated this week
- π π« Trim, circularise and orient long read bacterial genome assembliesβ24Sep 7, 2019Updated 6 years ago
- Influenza data pipeline to automate genotyping assignmentβ39Oct 14, 2025Updated 4 months ago
- Viral genome alignment, mutation calling, clade assignment, quality checks and phylogenetic placementβ250Feb 5, 2026Updated 3 weeks ago
- IRMA (the Iterative Refinement Meta-Assembler) is a highly configurable and adaptive tool for virus genome assembly.β23Dec 19, 2025Updated 2 months ago