LYVE-SET, a method of using hqSNPs to create a phylogeny, especially for outbreak investigations
☆26Aug 26, 2024Updated last year
Alternatives and similar repositories for lyve-SET
Users that are interested in lyve-SET are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- UPHL's Reference Free Pipeline☆29Jul 17, 2026Updated last week
- The R package 'phylosamp' implements novel tools that estimate the probability of transmission between two cases given phylogenetic linka…☆14May 23, 2023Updated 3 years ago
- tool to determine optimal refrerence genome given a set of fasta files☆15May 18, 2023Updated 3 years ago
- Bacterial surveillance pipeline.☆28Jul 10, 2026Updated 2 weeks ago
- 🧬 💻 TOSTADAS → Toolkit for Open Sequence Triage, Annotation and DAtabase Submission☆29Mar 10, 2026Updated 4 months ago
- Deploy to Railway using AI coding agents - Free Credits Offer • AdUse Claude Code, Codex, OpenCode, and more. Autonomous software development now has the infrastructure to match with Railway.
- ☆16Oct 2, 2019Updated 6 years ago
- A Nextflow pipeline for viral genomics (Influenza/RSV) supporting Illumina and Nanopore sequencing of clinical and wastewater samples.☆10Jun 9, 2026Updated last month
- Experiments with using BIGSI data structure for metagenomic and QC applications☆19Aug 12, 2024Updated last year
- A taxonomic classifier of plasmids☆28Jul 7, 2021Updated 5 years ago
- Salmonella serotyping from genome sequencing data☆11Sep 3, 2018Updated 7 years ago
- SeqSero2☆41Oct 1, 2025Updated 9 months ago
- Nextflow workflows to assign Salmonella serotype based on Genome similarity using MASH, SOURMASH and KMA.☆13Jul 2, 2026Updated 3 weeks ago
- ☆10Apr 16, 2025Updated last year
- The Genomic Epidemiology Application Ontology describes the genomics, laboratory, clinical and epidemiological contextual information req…☆25Jul 11, 2026Updated 2 weeks ago
- Managed Database hosting by DigitalOcean • AdPostgreSQL, MySQL, MongoDB, Kafka, Valkey, and OpenSearch available. Automatically scale up storage and focus on building your apps.
- Static website for the PH4AGE alliance☆13Oct 27, 2023Updated 2 years ago
- CFSAN Shigella Typing Pipeline☆15Jun 11, 2026Updated last month
- A methodology to rapidly leverage whole genome sequencing of bacterial isolates for clinical identification.☆35Jul 11, 2026Updated 2 weeks ago
- software to identify primers that can distinguish genomes☆20Jan 23, 2026Updated 6 months ago
- ☆23Updated this week
- k-mer based Pipeline to identify the Serotype from Illumina NGS reads☆27Jul 13, 2023Updated 3 years ago
- A pipeline for high-quality bacterial genome construction using ONT sequencing☆40Sep 22, 2022Updated 3 years ago
- Output FASTQ summary statistics in JSON format☆29Oct 30, 2022Updated 3 years ago
- Automated Pipeline to Generate FTP Files and Manage Submission of Sequence Data to Public Repositories☆40Feb 20, 2026Updated 5 months ago
- Deploy on Railway without the complexity - Free Credits Offer • AdConnect your repo and Railway handles the rest with instant previews. Quickly provision container image services, databases, and storage volumes.
- Pipeline to generate NGS reads from a phylogeny☆39Sep 13, 2022Updated 3 years ago
- Influenza genome analysis Nextflow workflow☆27Jun 3, 2026Updated last month
- ☆23Apr 2, 2026Updated 3 months ago
- Cluster informed Shigella and EIEC serotyping tool from Illumina reads and assemblies☆14Jun 30, 2023Updated 3 years ago
- emm Automatic Isolate Labeller☆15Mar 25, 2025Updated last year
- 🧮 🔢 Generate multi-sample k-mer count matrix from WGS☆11Jan 17, 2026Updated 6 months ago
- SNP Pipeline is a pipeline for the production of SNP matrices from sequence data used in the phylogenetic analysis of pathogenic organism…☆67Jun 11, 2026Updated last month
- Assign genotypes to Salmonella Typhi genomes based on VCF files (mapped to Typhi CT18 reference genome)☆30Jul 18, 2025Updated last year
- ☆13May 27, 2025Updated last year
- Managed Database hosting by DigitalOcean • AdPostgreSQL, MySQL, MongoDB, Kafka, Valkey, and OpenSearch available. Automatically scale up storage and focus on building your apps.
- ☆27Aug 2, 2023Updated 2 years ago
- Intra-species bacterial contamination detection☆26Jul 10, 2026Updated 2 weeks ago
- Spriggan is a pipeline used for assembly of bacterial whole genome sequence data and identification of antibiotic resistance genes.☆16Jul 9, 2026Updated 2 weeks ago
- Bioinformatics workflows for genomic characterization, submission preparation, and genomic epidemiology of viral pathogens of concern, es…☆42Aug 5, 2024Updated last year
- A message queue for genomic surveillance☆20Oct 14, 2021Updated 4 years ago
- In silico prediction of E. coli serotype, pathotype and shiga toxin subtyping☆66Jun 5, 2025Updated last year
- BSR-Based Allele Calling Algorithm☆149Updated this week