Code Safety Inspection Service
☆20Sep 23, 2022Updated 3 years ago
Alternatives and similar repositories for CSIS
Users that are interested in CSIS are comparing it to the libraries listed below
Sorting:
- emm Automatic Isolate Labeller☆12Mar 25, 2025Updated 11 months ago
- A simple nextflow pipeline for running kraken2 and bracken in a docker container☆20Oct 8, 2025Updated 5 months ago
- Rapid identification of Staphylococcus aureus agr locus type and agr operon variants.☆10Jan 6, 2023Updated 3 years ago
- Metagenomics/viromics pipeline that focuses on automation, user-friendliness and a clear audit trail. Jovian aims to empower classical bi…☆18Sep 1, 2023Updated 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
- List and download schemes from pubMLST.org and other BIGSDB servers☆10Oct 14, 2024Updated last year
- Automated Pipeline to Generate FTP Files and Manage Submission of Sequence Data to Public Repositories☆39Feb 20, 2026Updated last month
- Bacterial surveillance pipeline.☆27Dec 30, 2025Updated 2 months ago
- ☆16Apr 29, 2024Updated last year
- CFSAN Shigella Typing Pipeline☆15Jul 6, 2023Updated 2 years ago
- GrapeTree is a fully interactive, tree visualization program, which supports facile manipulations of both tree layout and metadata. Click…☆87Dec 15, 2024Updated last year
- Get microbial sequence data easier and faster☆28Nov 7, 2019Updated 6 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…☆53Jul 24, 2025Updated 7 months ago
- ASMNGS20 - 2020 Conference Details☆15Jun 10, 2022Updated 3 years ago
- StxTyper uses a standardized algorithm to accurately type both known and unknown Shiga toxin operons from assembled genomic sequence.☆17Dec 9, 2025Updated 3 months ago
- Dryad is a Nextflow pipeline for examining prokaryote relatedness. Dryad can perform a reference free analysis and/or SNP analysis.☆18Updated this week
- Static website for the PH4AGE alliance☆13Oct 27, 2023Updated 2 years ago
- Precise host read removal☆119Sep 4, 2025Updated 6 months ago
- Intra-species bacterial contamination detection☆25Feb 5, 2026Updated last month
- Fasten toolkit, for streaming operations on fastq files☆81Oct 24, 2025Updated 4 months ago
- rapid serotyping of Vibrio parahaemolyticus from whole genome sequencing data using serogroup-specific genes☆10Sep 2, 2021Updated 4 years ago
- GRIMER performs analysis of microbiome studies and generates a portable and interactive dashboard integrating annotation, taxonomy and me…☆24Feb 6, 2023Updated 3 years ago
- A Nextflow pipeline for viral genomics (Influenza/RSV) supporting Illumina and Nanopore sequencing of clinical and wastewater samples.☆10Feb 27, 2026Updated 3 weeks ago
- A tool for exploring large trees in the browser☆124Mar 7, 2026Updated 2 weeks ago
- Benchmarking different ways of doing read (taxonomic) classification, with a focus on removal of contamination and MTB classification☆14Apr 8, 2024Updated last year
- A methodology to rapidly leverage whole genome sequencing of bacterial isolates for clinical identification.☆35Dec 2, 2024Updated last year
- Nextflow workflows to assign Salmonella serotype based on Genome similarity using MASH, SOURMASH and KMA.☆13Dec 24, 2025Updated 2 months ago
- interactive barplot for amplicon sequencing☆13Dec 5, 2024Updated last year
- A repo with just adapter sequences☆15Jul 7, 2025Updated 8 months ago
- UPHL's Reference Free Pipeline☆27Updated this week
- Evolutionary Bioinformatics Toolkit (EBT)☆12Jul 14, 2020Updated 5 years ago
- LYVE-SET, a method of using hqSNPs to create a phylogeny, especially for outbreak investigations☆27Aug 26, 2024Updated last year
- Assign genotypes to Salmonella Typhi genomes based on VCF files (mapped to Typhi CT18 reference genome)☆29Jul 18, 2025Updated 8 months ago
- Snakemake workflow for scoring and comparing multiple bacterial genome assemblies (Illumina, Nanopore) to reference genome(s).☆26Apr 5, 2024Updated last year
- Fast and precise comparison of genomes and metagenomes (in the order of terabytes) on a typical personal laptop☆74Jul 31, 2025Updated 7 months ago
- NCBI Pathogen Detection Portal toolkit☆11Sep 6, 2023Updated 2 years ago
- A proof of concept daisy-chaining Nextflow workflows☆31Mar 10, 2026Updated last week
- Output FASTQ summary statistics in JSON format☆29Oct 30, 2022Updated 3 years ago
- A streamlined workflow and GUI for real-time species identification and pathogen characterization via nanopore sequencing data. Engineere…☆20Oct 4, 2024Updated last year