CFSAN Shigella Typing Pipeline
☆15Jun 11, 2026Updated 3 months 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.☆14Updated this week
- Cluster informed Shigella and EIEC serotyping tool from Illumina reads and assemblies☆14Jun 30, 2023Updated 3 years ago
- A Nextflow pipeline for viral genomics (Influenza/RSV) supporting Illumina and Nanopore sequencing of clinical and wastewater samples.☆10Jun 9, 2026Updated 3 months ago
- Assign genotypes to Salmonella Typhi genomes based on VCF files (mapped to Typhi CT18 reference genome)☆30Jul 18, 2025Updated last year
- In silico serotyping, finetyping and Bexsero antigen sequence typing of Neisseria meningitidis☆17Feb 19, 2026Updated 7 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.
- Pneumococcal Capsular Typing tool for NGS data☆18Apr 6, 2021Updated 5 years ago
- rapid serotyping of Vibrio parahaemolyticus from whole genome sequencing data using serogroup-specific genes☆10Sep 2, 2021Updated 5 years ago
- ☆10Apr 16, 2025Updated last year
- ☆15May 22, 2025Updated last year
- Intra-species bacterial contamination detection☆26Jul 10, 2026Updated 2 months ago
- SISTR (Salmonella In Silico Typing Resource) command-line tool☆38Apr 24, 2025Updated last year
- SeqSero2☆41Oct 1, 2025Updated 11 months ago
- Bioinformatics workflows for genomic characterization, submission preparation, and genomic epidemiology of viral pathogens of concern, es…☆42Aug 5, 2024Updated 2 years ago
- tool to determine optimal refrerence genome given a set of fasta files☆15May 18, 2023Updated 3 years ago
- End-to-end encrypted cloud storage - Proton Drive • AdSpecial offer: 40% Off Yearly / 80% Off First Month. Protect your most important files, photos, and documents from prying eyes.
- ☆28Aug 2, 2023Updated 3 years ago
- An SRA tool that takes as input local fastq file from a clinical infection sample, identifies and removes any significant human read, and…☆57Jul 24, 2025Updated last year
- Experiments with using BIGSI data structure for metagenomic and QC applications☆19Aug 12, 2024Updated 2 years ago
- A simple pipeline for bacterial assembly and quality control☆17Sep 17, 2026Updated last week
- 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
- UPHL's Reference Free Pipeline☆29Sep 4, 2026Updated 3 weeks ago
- k-mer based Pipeline to identify the Serotype from Illumina NGS reads☆27Jul 13, 2023Updated 3 years ago
- interactive barplot for amplicon sequencing☆13Dec 5, 2024Updated last year
- Output FASTQ summary statistics in JSON format☆29Oct 30, 2022Updated 3 years ago
- Wordpress hosting with auto-scaling - Free Trial Offer • AdFully Managed hosting for WordPress and WooCommerce businesses that need reliable, auto-scalable performance. Cloudways SafeUpdates now available.
- Fast implementation of the Neighbour-Joining method for phylogenetic inference☆21Sep 10, 2024Updated 2 years ago
- Rapid identification of Staphylococcus aureus agr locus type and agr operon variants.☆14Jan 6, 2023Updated 3 years ago
- Predicting plasmid contigs from assemblies using single copy marker genes, plasmid genes, kmers - Developed by Linda van der Graaf☆51Sep 4, 2026Updated 3 weeks ago
- MutTui pipeline to reconstruct mutational spectra for bacterial and viral datasets☆35Jul 27, 2026Updated 2 months ago
- ☆22Jun 1, 2026Updated 3 months ago
- Phylotype your strains using Clermont's 2013 method: ezclermont.org☆18May 5, 2026Updated 4 months ago
- Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins☆225Aug 27, 2025Updated last year
- A pipeline for high-quality bacterial genome construction using ONT sequencing☆40Sep 22, 2022Updated 4 years ago
- BACTpipe: An assembly and annotation pipeline for bacterial genomics☆21Aug 13, 2026Updated last month
- Managed Database hosting by DigitalOcean • AdPostgreSQL, MySQL, MongoDB, Kafka, Valkey, and OpenSearch available. Automatically scale up storage and focus on building your apps.
- Snakemake workflow for scoring and comparing multiple bacterial genome assemblies (Illumina, Nanopore) to reference genome(s).☆28May 7, 2026Updated 4 months ago
- A simple nextflow pipeline for running kraken2 and bracken in a docker container☆22Oct 8, 2025Updated 11 months ago
- The tool for in silico serotyping☆65Sep 20, 2026Updated last week
- Influenza genome analysis Nextflow workflow☆28Jun 3, 2026Updated 3 months ago
- SARS-CoV-2: detecting recombinations in viruses using large data sets with high sequence similarity☆13Aug 14, 2023Updated 3 years ago
- BRICK creates a BRIG-like interactive data visualisation for bacterial genome annotations and comparisons☆22Sep 9, 2026Updated 2 weeks ago
- Rapid determination of appropriate reference genomes.☆104Jan 22, 2025Updated last year