josephhughes / DiversiToolsView external linksLinks
Tool for analysing viral diversity from High Throughput Sequencing
☆12Nov 20, 2025Updated 2 months ago
Alternatives and similar repositories for DiversiTools
Users that are interested in DiversiTools are comparing it to the libraries listed below
Sorting:
- SaffronTree: Reference free rapid phylogenetic tree construction from raw read data☆25Jun 11, 2020Updated 5 years ago
- Quasitools is a collection of tools for analysing viral quasispecies data.☆27Nov 25, 2021Updated 4 years ago
- Computes a consensus sequence with wobbles, ambiguous bases, and in-frame insertions, from a NGS read alignment.☆18May 14, 2018Updated 7 years ago
- Local Lineage and Monophyly Assessment☆16Aug 5, 2021Updated 4 years ago
- Rapid identification of Staphylococcus aureus agr locus type and agr operon variants.☆10Jan 6, 2023Updated 3 years ago
- ☆12Feb 15, 2023Updated 2 years ago
- Tools for analyzing and comparing SARS-CoV-2 phylogenies☆10Nov 21, 2020Updated 5 years ago
- ☆10Dec 22, 2025Updated last month
- Set of tools for viral metagenomics.☆14Jan 21, 2026Updated 3 weeks ago
- ☆11Jun 29, 2023Updated 2 years ago
- A MinION-based pipeline for tracking species biodiversity☆13Feb 19, 2024Updated last year
- Collection of R scripts for SARS-CoV-2 (variant) analyses☆12Mar 2, 2023Updated 2 years ago
- A nextflow version of the Wochenende reference metagenome binning and visualization pipeline☆15Dec 14, 2024Updated last year
- BEAST+BEAGLE compiled with NVIDIA CUDA☆12Jul 19, 2024Updated last year
- Raspir, the rare species identifier☆11Oct 19, 2023Updated 2 years ago
- design common and specific primer for LAMP using the whole genome☆14Oct 8, 2019Updated 6 years ago
- A tool easily taken advantage of for in silico serogrouping of Pseudomonas aeruginosa isolates☆13Aug 26, 2024Updated last year
- Simple Manipulation Of Trees☆13Aug 16, 2025Updated 5 months ago
- 🧬 Viral genome reference alignment☆12Jan 26, 2021Updated 5 years ago
- Base for the Viral Genomics and Bioinformatics Repository☆17Jul 5, 2024Updated last year
- Pipeline to automatically analyse SARS-CoV-2 Whole genome sequencing Illumina data obtained using EasySeq SARS-CoV-2/COVID-19 Whole Geno…☆15Jul 26, 2022Updated 3 years 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
- Surveillance of pathogens using population genomics and sequencing☆54Feb 6, 2026Updated last week
- An `R` package for various phylogenetic and evolutionary biology data manipulations☆12Mar 5, 2018Updated 7 years ago
- R tools to interact with hap.py output☆16Jul 12, 2019Updated 6 years ago
- Report salient qPCR primer/probe or immune epitope mismatches info against a set of pathogen isolate genomes☆16Mar 11, 2025Updated 11 months ago
- Welcome to the StrainHub Repo - Files and Data - StrainHub Online:☆17Jun 26, 2022Updated 3 years ago
- ☆16May 22, 2023Updated 2 years ago
- Prediction of B-cell epitopes from amino acid sequences using deep neural networks.☆18Sep 7, 2022Updated 3 years ago
- Prediction of B-cell epitopes from amino acid sequences using deep neural networks.☆16Aug 3, 2021Updated 4 years ago
- Miscellaneous scripts☆24Sep 7, 2016Updated 9 years ago
- Primer3Web is a simple web interface to primer3.☆17Aug 18, 2021Updated 4 years ago
- Reconstruction of transmission trees using genomic data☆72Sep 27, 2023Updated 2 years ago
- Small pipeline to cluster viral genomes based on their k-mer content. WiP☆18Feb 3, 2026Updated last week
- finding conserved regions in highly diverse genomes☆15Jun 1, 2025Updated 8 months ago
- Program for estimating πN/πS, dN/dS, and other diversity measures from next-generation sequencing data☆120Aug 21, 2023Updated 2 years ago
- A tool in order to accurately remove primer sequences from NGS reads in an amplicon experiment☆20Nov 12, 2025Updated 3 months ago
- Tutorial for bacterial GWAS pipline and bugwas, created for Bodega Bay 2016 NGS workshop☆18Feb 12, 2016Updated 10 years ago
- deduplicate FASTA and FASTQ files☆22Feb 16, 2022Updated 3 years ago