Scripts and reference files to type streptococcus pneumoniae
☆11Aug 31, 2026Updated 2 months ago
Alternatives and similar repositories for Spn_Scripts_Reference
Users that are interested in Spn_Scripts_Reference are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- In silico Penicillin Binding Protein (PBP) typer for Streptococcus pneumoniae assemblies☆10Aug 6, 2024Updated 2 years ago
- In silico multi-antigen sequence typing for Neisseria gonorrhoeae (NG-MAST)☆10Jun 17, 2026Updated 4 months ago
- JUNIPER: Large-Scale Outbreak Reconstruction☆14Mar 26, 2025Updated last year
- A Nextflow pipeline for viral genomics (Influenza/RSV) supporting Illumina and Nanopore sequencing of clinical and wastewater samples.☆10Oct 27, 2026Updated last week
- QA/QC pipeline for a MiSeq/HiSeq/Ion Torrent/assembly-only run☆12Dec 2, 2024Updated last year
- 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.
- ☆13Oct 26, 2026Updated last week
- A tool for managing your pores☆10Jul 22, 2026Updated 3 months ago
- A tool in order to accurately remove primer sequences from NGS reads in an amplicon experiment☆20Nov 12, 2025Updated 11 months ago
- Genomic neighbor typing of bacterial pathogens using MinHash☆42Jan 10, 2023Updated 3 years ago
- Static website for the PH4AGE alliance☆14Oct 27, 2023Updated 3 years ago
- Nextflow workflows to assign Salmonella serotype based on Genome similarity using MASH, SOURMASH and KMA.☆15Sep 29, 2026Updated last month
- Development moved to https://gitlab.com/cgps/tools/qualibact. QC cutoffs for bacterial genomes.☆19Updated this week
- emm Automatic Isolate Labeller☆16Mar 25, 2025Updated last year
- Spriggan is a pipeline used for assembly of bacterial whole genome sequence data and identification of antibiotic resistance genes.☆16Updated this week
- AI Agents on 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.
- Cluster informed Shigella and EIEC serotyping tool from Illumina reads and assemblies☆14Jun 30, 2023Updated 3 years ago
- Fasten toolkit, for streaming operations on fastq files☆85Oct 12, 2026Updated 3 weeks ago
- ☆23Sep 22, 2026Updated last month
- Nextflow pipeline for species-specific typing of bacteria☆11Oct 13, 2026Updated 3 weeks ago
- Databases for wg/cgMLST analysis with the PN2.0 software☆10May 7, 2026Updated 5 months ago
- A Nextflow pipeline for fast and accurate SNP distance estimation from WGS read data or genome assemblies☆11Jun 11, 2026Updated 4 months ago
- Predict MLST directly from uncorrected long reads☆28Oct 31, 2025Updated last year
- UPHL's Reference Free Pipeline☆29Updated this week
- Bayesian inference of ancestral dates on bacterial phylogenetic trees☆99Dec 9, 2025Updated 10 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.
- A tool to aid virus sequencing and accelerate IRMA.☆13Updated this week
- A tool for typing SCCmec cassettes in assemblies☆14Aug 25, 2024Updated 2 years ago
- NCBI Pathogen Detection Portal toolkit☆11Sep 6, 2023Updated 3 years ago
- The repository contains the source code of the NanoForms server (Czmil et al. NanoForms: an integrated server for processing, analysis an…☆11Feb 22, 2023Updated 3 years ago
- REcombination BARcode detector.☆17Apr 2, 2024Updated 2 years ago
- Disty McMatrixface - compute a distance matrix from a core genome alignment file☆15Mar 15, 2023Updated 3 years ago
- A Python package for working with Bactopia☆12Aug 5, 2026Updated 3 months ago
- ☆26Oct 17, 2018Updated 8 years ago
- Nextflow pipeline for bacterial clustering and linkage detection based on core genome analysis, designed to support genomic surveillance …☆12Updated this week
- 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.
- Sketch-based surveillance platform☆13Oct 29, 2026Updated last week
- Extracts contigs harbouring a target gene / sequence from assemblies and aligns the contigs around the target sequence☆13May 15, 2018Updated 8 years ago
- Private, browser-based placement of genome sequences on phylogenetic trees using UShER.☆11Aug 12, 2026Updated 2 months ago
- The Pathogenwatch Vibrio cholerae genotyping tool☆11Oct 9, 2026Updated 3 weeks ago
- Benchmark and toy datasets☆12Jan 8, 2025Updated last year
- Extract subsets of ONT (Nanopore) reads based on time☆26Sep 12, 2024Updated 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