Cluster informed Shigella and EIEC serotyping tool from Illumina reads and assemblies
☆13Jun 30, 2023Updated 3 years ago
Alternatives and similar repositories for ShigEiFinder
Users that are interested in ShigEiFinder are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- CFSAN Shigella Typing Pipeline☆15Jun 11, 2026Updated 3 weeks ago
- A methodology to rapidly leverage whole genome sequencing of bacterial isolates for clinical identification.☆35Dec 2, 2024Updated last year
- A Nextflow pipeline for viral genomics (Influenza/RSV) supporting Illumina and Nanopore sequencing of clinical and wastewater samples.☆10Jun 9, 2026Updated 3 weeks ago
- In silico serotyping, finetyping and Bexsero antigen sequence typing of Neisseria meningitidis☆15Feb 19, 2026Updated 4 months ago
- ☆10Apr 16, 2025Updated last year
- GPUs on demand by Runpod - Special Offer Available • AdRun AI, ML, and HPC workloads on powerful cloud GPUs—without limits or wasted spend. Deploy GPUs in under a minute and pay by the second.
- SARS-CoV-2: detecting recombinations in viruses using large data sets with high sequence similarity☆13Aug 14, 2023Updated 2 years ago
- An `R` package for various phylogenetic and evolutionary biology data manipulations☆12Mar 5, 2018Updated 8 years ago
- A pipeline for bioinformatics analysis of bacterial genomes☆34Updated this week
- Genomic neighbor typing of bacterial pathogens using MinHash☆42Jan 10, 2023Updated 3 years ago
- Intra-species bacterial contamination detection☆25Apr 13, 2026Updated 2 months ago
- Assign genotypes to Salmonella Typhi genomes based on VCF files (mapped to Typhi CT18 reference genome)☆30Jul 18, 2025Updated 11 months ago
- Dadaist2 🟨 Highway to R☆13Mar 7, 2025Updated last year
- Microbial agile accurate SNP Typer☆30Dec 27, 2023Updated 2 years ago
- Predict plasmids from uncorrected long read data☆41Feb 27, 2026Updated 4 months ago
- Managed Kubernetes at scale on DigitalOcean • AdDigitalOcean Kubernetes includes the control plane, bandwidth allowance, container registry, automatic updates, and more for free.
- frame-shift correction for long-read (meta)genomics☆33Dec 11, 2023Updated 2 years ago
- High-quality Nanopore-only genome polisher☆71Aug 16, 2024Updated last year
- SISTR (Salmonella In Silico Typing Resource) command-line tool☆35Apr 24, 2025Updated last year
- ☆17May 22, 2023Updated 3 years ago
- In silico prediction of E. coli serotype, pathotype and shiga toxin subtyping☆66Jun 5, 2025Updated last year
- Extract subsets of ONT (Nanopore) reads based on time☆24Sep 12, 2024Updated last year
- VIGOR4☆22Aug 15, 2025Updated 10 months ago
- Nextflow workflows to assign Salmonella serotype based on Genome similarity using MASH, SOURMASH and KMA.☆13Updated this week
- UPHL's Reference Free Pipeline☆29May 22, 2026Updated last month
- 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.
- Fast DNA search and [host] depletion using minimizers☆113Jun 24, 2026Updated last week
- Multi-platform genome assembly pipeline for Illumina, Nanopore and PacBio reads☆65Jan 22, 2026Updated 5 months ago
- Predict MLST directly from uncorrected long reads☆27Oct 31, 2025Updated 8 months ago
- ☆22Jun 1, 2026Updated last month
- An SRA tool that takes as input local fastq file from a clinical infection sample, identifies and removes any significant human read, and…☆54Jul 24, 2025Updated 11 months ago
- A simple nextflow pipeline for running kraken2 and bracken in a docker container☆21Oct 8, 2025Updated 8 months ago
- SeqSero2☆40Oct 1, 2025Updated 9 months ago
- Sketch-based surveillance platform☆14Updated this week
- 🧬 💻 TOSTADAS → Toolkit for Open Sequence Triage, Annotation and DAtabase Submission☆29Mar 10, 2026Updated 3 months ago
- Serverless GPU API endpoints on Runpod - Get Bonus Credits • AdSkip the infrastructure headaches. Auto-scaling, pay-as-you-go, no-ops approach lets you focus on innovating your application.
- app to collapse Pango lineages for reporting☆13Dec 9, 2025Updated 6 months ago
- A tool in order to accurately remove primer sequences from NGS reads in an amplicon experiment☆20Nov 12, 2025Updated 7 months ago
- C++ tools for NCBI taxonomy tasks☆12Jun 26, 2025Updated last year
- Rapid identification of Staphylococcus aureus agr locus type and agr operon variants.☆13Jan 6, 2023Updated 3 years ago
- A tool easily taken advantage of for in silico serogrouping of Pseudomonas aeruginosa isolates☆14Aug 26, 2024Updated last year
- A pipeline for high-quality bacterial genome construction using ONT sequencing☆40Sep 22, 2022Updated 3 years ago
- TAXnomic Profile Aggregation and STAndardisation☆44May 2, 2026Updated 2 months ago