Pneumococcal Capsular Typing tool for NGS data
☆18Apr 6, 2021Updated 4 years ago
Alternatives and similar repositories for PneumoCaT
Users that are interested in PneumoCaT are comparing it to the libraries listed below
Sorting:
- k-mer based Pipeline to identify the Serotype from Illumina NGS reads☆25Jul 13, 2023Updated 2 years ago
- Nextflow workflows to assign Salmonella serotype based on Genome similarity using MASH, SOURMASH and KMA.☆13Dec 24, 2025Updated 2 months ago
- CFSAN Shigella Typing Pipeline☆15Jul 6, 2023Updated 2 years ago
- in silico typing of the H. influenzae cap locus☆12Jul 15, 2024Updated last year
- A Nextflow pipeline for viral genomics (Influenza/RSV) supporting Illumina and Nanopore sequencing of clinical and wastewater samples.☆10Feb 27, 2026Updated last week
- ☆10Apr 16, 2025Updated 10 months ago
- ☆59Feb 23, 2026Updated last week
- Extract subsets of ONT (Nanopore) reads based on time☆23Sep 12, 2024Updated last year
- emm Automatic Isolate Labeller☆12Mar 25, 2025Updated 11 months ago
- Assign genotypes to Salmonella Typhi genomes based on VCF files (mapped to Typhi CT18 reference genome)☆29Jul 18, 2025Updated 7 months ago
- SISTR (Salmonella In Silico Typing Resource) command-line tool☆32Apr 24, 2025Updated 10 months ago
- ☆27Aug 2, 2023Updated 2 years ago
- ☆21Jan 23, 2026Updated last month
- Predicting plasmid contigs from assemblies using single copy marker genes, plasmid genes, kmers - Developed by Linda van der Graaf☆50Apr 16, 2024Updated last year
- Assign genotypes to Salmonella Paratyphi A isolates using their whole-genome data.☆10Mar 6, 2025Updated last year
- IS mapping software☆57Dec 3, 2021Updated 4 years ago
- ☆20Feb 12, 2026Updated 3 weeks ago
- In silico taxonomic classification of Bacillus cereus group genomes using whole-genome sequencing data☆22May 8, 2024Updated last year
- A simple nextflow pipeline for running kraken2 and bracken in a docker container☆20Oct 8, 2025Updated 4 months ago
- Recombination-free trees☆63Sep 1, 2025Updated 6 months ago
- rapid serotyping of Vibrio parahaemolyticus from whole genome sequencing data using serogroup-specific genes☆10Sep 2, 2021Updated 4 years ago
- Detecting recombination of viral lineages☆11Dec 23, 2025Updated 2 months ago
- Predict plasmids from uncorrected long read data☆41Feb 27, 2026Updated last week
- Genomic neighbor typing of bacterial pathogens using MinHash☆42Jan 10, 2023Updated 3 years ago
- Rapid identification of Staphylococcus aureus agr locus type and agr operon variants.☆10Jan 6, 2023Updated 3 years ago
- ☆136Feb 26, 2026Updated last week
- Bacterial surveillance pipeline.☆27Dec 30, 2025Updated 2 months ago
- BRICK creates a BRIG-like interactive data visualisation for bacterial genome annotations and comparisons☆21Dec 9, 2025Updated 2 months ago
- ☆22Feb 2, 2026Updated last month
- Standalone Python re-implementation of the POLCA polisher from MaSuRCA☆44Aug 20, 2025Updated 6 months ago
- ☆11Mar 10, 2024Updated last year
- A microbial genomic analysis pipeline used by the Djordjevic Lab☆13Feb 9, 2025Updated last year
- Cluster informed Shigella and EIEC serotyping tool from Illumina reads and assemblies☆12Jun 30, 2023Updated 2 years ago
- NCBI Pathogen Detection Portal toolkit☆11Sep 6, 2023Updated 2 years ago
- A taxonomic classifier of plasmids☆28Jul 7, 2021Updated 4 years ago
- Bioinformatics workflows for genomic characterization, submission preparation, and genomic epidemiology of pathogens of public health con…☆61Feb 27, 2026Updated last week
- UPHL's Reference Free Pipeline☆27Feb 27, 2026Updated last week
- In silico serotyping, finetyping and Bexsero antigen sequence typing of Neisseria meningitidis☆15Feb 19, 2026Updated 2 weeks ago
- Generate basic stats for an assembly.☆13Feb 12, 2023Updated 3 years ago