☆20Apr 2, 2025Updated 11 months ago
Alternatives and similar repositories for DENV_pipeline
Users that are interested in DENV_pipeline are comparing it to the libraries listed below
Sorting:
- The R package 'phylosamp' implements novel tools that estimate the probability of transmission between two cases given phylogenetic linka…☆13May 23, 2023Updated 2 years ago
- SARs-CoV-2 Primer schemes☆16May 14, 2025Updated 9 months ago
- ☆29Jul 9, 2025Updated 7 months ago
- ☆25Jun 25, 2024Updated last year
- Rapid identification of Staphylococcus aureus agr locus type and agr operon variants.☆10Jan 6, 2023Updated 3 years ago
- Software for the Tree-Based Scan Statistic☆14Updated this week
- Bacterial surveillance pipeline.☆27Dec 30, 2025Updated 2 months ago
- ☆22Feb 2, 2026Updated last month
- Fast, scalable, accurate and accessible Bayesian phylogenetics☆42Feb 23, 2026Updated last week
- A Nextflow pipeline for viral genomics (Influenza/RSV) supporting Illumina and Nanopore sequencing of clinical and wastewater samples.☆10Feb 27, 2026Updated last week
- Materials for the course on Bayesian model building run at Second Faculty of Medicine at Charles University in Prague☆11May 6, 2024Updated last year
- Tools for analyzing and comparing SARS-CoV-2 phylogenies☆10Nov 21, 2020Updated 5 years ago
- Nextstrain build for dengue virus☆13Dec 16, 2025Updated 2 months ago
- UPHL's Reference Free Pipeline☆27Feb 27, 2026Updated last week
- ☆13Nov 1, 2022Updated 3 years ago
- Renders SVG schema of SARS-CoV-2 clade as defined by Nextstrain☆16Nov 24, 2025Updated 3 months ago
- Nanopore read de-multiplexer☆13Mar 25, 2020Updated 5 years ago
- Bayesian nowcasting with adjustment for delayed and incomplete reporting to estimate COVID-19 infections in the United States☆27Aug 14, 2025Updated 6 months ago
- Small collection of tools for performing quality control on coronavirus sequencing data and genomes☆49Apr 25, 2024Updated last year
- Tools and tutorials for multi-level regression and post-stratification of survey data☆11Mar 5, 2024Updated 2 years ago
- emm Automatic Isolate Labeller☆12Mar 25, 2025Updated 11 months ago
- Repository for reproducing results in structured priors MRP paper☆17Jun 27, 2020Updated 5 years ago
- An R package for Bayes Linear emulation and history matching.☆18Dec 1, 2025Updated 3 months ago
- Reference-based consensus creation☆59Feb 10, 2026Updated 3 weeks 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…☆36May 1, 2022Updated 3 years ago
- Olivar: towards automated variant aware primer design for multiplex tiled amplicon sequencing of pathogens☆38Jan 22, 2026Updated last month
- ☆13Oct 30, 2024Updated last year
- Scripts and data for Modelling reporting delay for disease surveillance data using Bayesian methods.☆16Jul 11, 2019Updated 6 years ago
- ☆21Feb 12, 2026Updated 3 weeks ago
- Splitting and accelerating the Oxford Nanopore basecaller guppy using CPU with the SLURM job scheduler☆16Jul 1, 2024Updated last year
- Collection template and associated materials for SARS-CoV-2 metadata☆37Oct 27, 2023Updated 2 years ago
- SARS-CoV-2 genomics☆16Jun 20, 2025Updated 8 months ago
- Bayesian spatio-temporal methods for small-area estimation of HIV indicators (PhD thesis, Imperial College London, 2023)☆16Nov 11, 2025Updated 3 months ago
- Gaussian processes on graphs and lattices in Stan.☆19Mar 17, 2025Updated 11 months ago
- IRMA (the Iterative Refinement Meta-Assembler) is a highly configurable and adaptive tool for virus genome assembly.☆23Dec 19, 2025Updated 2 months ago
- StxTyper uses a standardized algorithm to accurately type both known and unknown Shiga toxin operons from assembled genomic sequence.☆17Dec 9, 2025Updated 2 months ago
- Munge GenBank files into FASTA and tab-separated metadata☆15Feb 5, 2026Updated last month
- Hidden Markov Models applied to basketball player tracking data☆18Oct 5, 2019Updated 6 years ago
- This repository houses the code to run SURPI+, a rapid computational pipeline for comprehensive identification of pathogens from clinical…☆42Nov 20, 2019Updated 6 years ago