In silico prediction of E. coli serotype, pathotype and shiga toxin subtyping
☆66Jun 5, 2025Updated last year
Alternatives and similar repositories for ecoli_serotyping
Users that are interested in ecoli_serotyping are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Assign genotypes to Salmonella Typhi genomes based on VCF files (mapped to Typhi CT18 reference genome)☆30Jul 18, 2025Updated 11 months ago
- SISTR (Salmonella In Silico Typing Resource) command-line tool☆35Apr 24, 2025Updated last year
- Clermont PCR method In-Silico☆25Feb 8, 2024Updated 2 years ago
- A pipeline for bioinformatics analysis of bacterial genomes☆34Jun 28, 2026Updated last week
- ☆142Jun 1, 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. Zero configuration with optimized deployments.
- In silico serotyping, finetyping and Bexsero antigen sequence typing of Neisseria meningitidis☆15Feb 19, 2026Updated 4 months ago
- whole genome MLST analysis☆53Jun 17, 2026Updated 2 weeks ago
- Cluster informed Shigella and EIEC serotyping tool from Illumina reads and assemblies☆14Jun 30, 2023Updated 3 years ago
- Nextflow workflows to assign Salmonella serotype based on Genome similarity using MASH, SOURMASH and KMA.☆13Updated this week
- rapid serotyping of Vibrio parahaemolyticus from whole genome sequencing data using serogroup-specific genes☆10Sep 2, 2021Updated 4 years ago
- Predict MLST directly from uncorrected long reads☆27Oct 31, 2025Updated 8 months ago
- A microbial genomic analysis pipeline used by the Djordjevic Lab☆13Feb 9, 2025Updated last year
- Experiments with using BIGSI data structure for metagenomic and QC applications☆19Aug 12, 2024Updated last year
- Genomic neighbor typing of bacterial pathogens using MinHash☆42Jan 10, 2023Updated 3 years ago
- 1-Click AI Models by DigitalOcean Gradient • AdDeploy popular AI models on DigitalOcean Gradient GPU virtual machines with just a single click. Zero configuration with optimized deployments.
- Scan contig files against PubMLST typing schemes☆288Jun 17, 2026Updated 2 weeks ago
- A pipeline for running AMRfinderPlus and collating results into functional classes☆100Jun 8, 2026Updated 3 weeks ago
- Mass screening of contigs for antimicrobial and virulence genes☆497Apr 3, 2026Updated 3 months ago
- ☆27Aug 2, 2023Updated 2 years ago
- MOB-suite: Software tools for clustering, reconstruction and typing of plasmids from draft assemblies☆177Apr 16, 2025Updated last year
- Melon: metagenomic long-read-based taxonomic identification and quantification using marker genes☆37Jun 4, 2026Updated last month
- CFSAN Shigella Typing Pipeline☆15Jun 11, 2026Updated 3 weeks ago
- a short-read polishing tool for long-read assemblies☆218Sep 19, 2025Updated 9 months ago
- The Genomic Epidemiology Application Ontology describes the genomics, laboratory, clinical and epidemiological contextual information req…☆25Jun 4, 2026Updated last month
- 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.
- Scans genome contigs against the ResFinder, PlasmidFinder, and PointFinder databases.☆201Jun 10, 2026Updated 3 weeks ago
- ☆33Updated this week
- Intra-species bacterial contamination detection☆25Apr 13, 2026Updated 2 months ago
- Mash MinHash search your nucleotide sequences against a NCBI RefSeq genomes database☆43Dec 11, 2020Updated 5 years ago
- Short Read Sequence Typing for Bacterial Pathogens☆148Jun 20, 2021Updated 5 years ago
- k-mer based Pipeline to identify the Serotype from Illumina NGS reads☆25Jul 13, 2023Updated 2 years ago
- Plasmid exploration of bacterial genomes☆26Mar 2, 2022Updated 4 years ago
- A tool for generating consensus long-read assemblies for bacterial genomes☆234Apr 27, 2026Updated 2 months ago
- VarSkip multiplex PCR designs for SARS-CoV-2 sequencing☆14Jun 14, 2022Updated 4 years 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.
- A Nextflow pipeline for viral genomics (Influenza/RSV) supporting Illumina and Nanopore sequencing of clinical and wastewater samples.☆10Jun 9, 2026Updated 3 weeks ago
- Pneumococcal Capsular Typing tool for NGS data☆18Apr 6, 2021Updated 5 years ago
- Predict plasmids from uncorrected long read data☆41Feb 27, 2026Updated 4 months ago
- A k-mer based program for the identification of known plasmids from whole-genome sequencing reads☆36Feb 3, 2021Updated 5 years ago
- Antimicrobial Resistance Identification By Assembly☆186Oct 12, 2023Updated 2 years ago
- LYVE-SET, a method of using hqSNPs to create a phylogeny, especially for outbreak investigations☆26Aug 26, 2024Updated last year
- BRICK creates a BRIG-like interactive data visualisation for bacterial genome annotations and comparisons☆22Dec 9, 2025Updated 6 months ago