CFSAN Shigella Typing Pipeline
☆15Jul 6, 2023Updated 2 years ago
Alternatives and similar repositories for shigatyper
Users that are interested in shigatyper are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Nextflow workflows to assign Salmonella serotype based on Genome similarity using MASH, SOURMASH and KMA.☆13Dec 24, 2025Updated 3 months ago
- Cluster informed Shigella and EIEC serotyping tool from Illumina reads and assemblies☆13Jun 30, 2023Updated 2 years ago
- A Nextflow pipeline for viral genomics (Influenza/RSV) supporting Illumina and Nanopore sequencing of clinical and wastewater samples.☆10Feb 27, 2026Updated last month
- Assign genotypes to Salmonella Typhi genomes based on VCF files (mapped to Typhi CT18 reference genome)☆29Jul 18, 2025Updated 8 months ago
- In silico serotyping, finetyping and Bexsero antigen sequence typing of Neisseria meningitidis☆15Feb 19, 2026Updated last month
- 1-Click AI Models by DigitalOcean Gradient • AdDeploy popular AI models on DigitalOcean Gradient GPU virtual machines with just a single click and start building anything your business needs.
- Pneumococcal Capsular Typing tool for NGS data☆18Apr 6, 2021Updated 4 years ago
- rapid serotyping of Vibrio parahaemolyticus from whole genome sequencing data using serogroup-specific genes☆10Sep 2, 2021Updated 4 years ago
- Intra-species bacterial contamination detection☆25Feb 5, 2026Updated last month
- ☆10Apr 16, 2025Updated 11 months ago
- ☆15May 22, 2025Updated 10 months ago
- SISTR (Salmonella In Silico Typing Resource) command-line tool☆33Apr 24, 2025Updated 11 months ago
- Bioinformatics workflows for genomic characterization, submission preparation, and genomic epidemiology of viral pathogens of concern, es…☆42Aug 5, 2024Updated last year
- SeqSero2☆40Oct 1, 2025Updated 5 months ago
- tool to determine optimal refrerence genome given a set of fasta files☆15May 18, 2023Updated 2 years ago
- 1-Click AI Models by DigitalOcean Gradient • AdDeploy popular AI models on DigitalOcean Gradient GPU virtual machines with just a single click and start building anything your business needs.
- ☆27Aug 2, 2023Updated 2 years ago
- Ampseer examines reads in fastq format and identifies which multiplex PCR primer set was used to generate the SARS-CoV-2 sequencing libra…☆15Feb 27, 2024Updated 2 years ago
- A simple pipeline for bacterial assembly and quality control☆16Mar 20, 2026Updated last week
- k-mer based Pipeline to identify the Serotype from Illumina NGS reads☆25Jul 13, 2023Updated 2 years ago
- UPHL's Reference Free Pipeline☆28Updated this week
- An SRA tool that takes as input local fastq file from a clinical infection sample, identifies and removes any significant human read, and…☆53Jul 24, 2025Updated 8 months ago
- Fast implementation of the Neighbour-Joining method for phylogenetic inference☆18Sep 10, 2024Updated last year
- Output FASTQ summary statistics in JSON format☆29Oct 30, 2022Updated 3 years ago
- interactive barplot for amplicon sequencing☆13Dec 5, 2024Updated last year
- DigitalOcean Gradient AI Platform • AdBuild production-ready AI agents using customizable tools or access multiple LLMs through a single endpoint. Create custom knowledge bases or connect external data.
- Rapid identification of Staphylococcus aureus agr locus type and agr operon variants.☆10Jan 6, 2023Updated 3 years ago
- Predicting plasmid contigs from assemblies using single copy marker genes, plasmid genes, kmers - Developed by Linda van der Graaf☆50Apr 16, 2024Updated last year
- MutTui pipeline to reconstruct mutational spectra for bacterial and viral datasets☆33Jul 2, 2024Updated last year
- ☆59Updated this week
- Phylotype your strains using Clermont's 2013 method: ezclermont.org☆15Aug 5, 2022Updated 3 years ago
- A pipeline for high-quality bacterial genome construction using ONT sequencing☆38Sep 22, 2022Updated 3 years ago
- Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins☆215Aug 27, 2025Updated 7 months ago
- BACTpipe: An assembly and annotation pipeline for bacterial genomics☆20Dec 3, 2024Updated last year
- Snakemake workflow for scoring and comparing multiple bacterial genome assemblies (Illumina, Nanopore) to reference genome(s).☆26Apr 5, 2024Updated last year
- 1-Click AI Models by DigitalOcean Gradient • AdDeploy popular AI models on DigitalOcean Gradient GPU virtual machines with just a single click and start building anything your business needs.
- ☆21Jan 23, 2026Updated 2 months ago
- A simple nextflow pipeline for running kraken2 and bracken in a docker container☆20Oct 8, 2025Updated 5 months ago
- Influenza data pipeline to automate genotyping assignment☆41Mar 19, 2026Updated last week
- BRICK creates a BRIG-like interactive data visualisation for bacterial genome annotations and comparisons☆21Dec 9, 2025Updated 3 months ago
- SARS-CoV-2: detecting recombinations in viruses using large data sets with high sequence similarity☆13Aug 14, 2023Updated 2 years ago
- Northern Arizona SNP Pipeline☆20Oct 29, 2024Updated last year
- NCBI Pathogen Detection Portal toolkit☆11Sep 6, 2023Updated 2 years ago