Experiments with using BIGSI data structure for metagenomic and QC applications
☆19Aug 12, 2024Updated last year
Alternatives and similar repositories for colorid
Users that are interested in colorid are comparing it to the libraries listed below
Sorting:
- Nextflow workflows to assign Salmonella serotype based on Genome similarity using MASH, SOURMASH and KMA.☆13Dec 24, 2025Updated 2 months ago
- ☆10Apr 16, 2025Updated 10 months ago
- Rapidly extract reads from a FASTQ file based on taxonomic classification via Kraken2.☆13Jan 26, 2026Updated last month
- A Nextflow pipeline for viral genomics (Influenza/RSV) supporting Illumina and Nanopore sequencing of clinical and wastewater samples.☆10Feb 27, 2026Updated last week
- BRICK creates a BRIG-like interactive data visualisation for bacterial genome annotations and comparisons☆21Dec 9, 2025Updated 3 months ago
- A tool easily taken advantage of for in silico serogrouping of Pseudomonas aeruginosa isolates☆13Aug 26, 2024Updated last year
- Visualize microbial evolution at the SNP level!☆15Aug 12, 2025Updated 6 months ago
- Sketch-based surveillance platform☆14Dec 17, 2024Updated last year
- A taxonomic classifier of plasmids☆28Jul 7, 2021Updated 4 years ago
- A surveillance-oriented tool to strengthen the linkage between pathogen genetic clusters and epidemiological data☆47Feb 20, 2026Updated 2 weeks ago
- Genomic neighbor typing of bacterial pathogens using MinHash☆42Jan 10, 2023Updated 3 years ago
- Automated Pipeline to Generate FTP Files and Manage Submission of Sequence Data to Public Repositories☆39Feb 20, 2026Updated 2 weeks ago
- Metagenomic Intra-Species Diversity Analysis (MIDAS)☆42Sep 3, 2024Updated last year
- REcombination BARcode detector.☆16Apr 2, 2024Updated last year
- Host depletion optimised for clinical metagenomic sequencing applications☆16Nov 18, 2024Updated last year
- tool to determine optimal refrerence genome given a set of fasta files☆15May 18, 2023Updated 2 years ago
- Predict MLST directly from uncorrected long reads☆27Oct 31, 2025Updated 4 months ago
- Organism-specific interpretation of AMR genotypes☆15Mar 13, 2024Updated last year
- Basecalling configuration prediction through FASTQ files☆33Nov 24, 2025Updated 3 months ago
- A pipeline for bioinformatics analysis of bacterial genomes☆32Updated this week
- Fast, accurate taxonomic assignments for the human vaginal microbiota☆11Feb 11, 2026Updated 3 weeks ago
- A simple pipeline for bacterial assembly and quality control☆16Feb 26, 2026Updated last week
- CFSAN Shigella Typing Pipeline☆15Jul 6, 2023Updated 2 years ago
- Population analysis PIPEline 🛠🧬☆22Mar 2, 2026Updated last week
- whole genome MLST analysis☆51Feb 26, 2026Updated last week
- taxonomic classifier based on the kraken2 algorithms and more☆46Dec 12, 2025Updated 2 months ago
- Compute bottom-s sketches and s-buckets sketches, using simd-minimizers crate.☆21Dec 3, 2025Updated 3 months ago
- Dryad is a Nextflow pipeline for examining prokaryote relatedness. Dryad can perform a reference free analysis and/or SNP analysis.☆18Nov 20, 2025Updated 3 months ago
- Indels are not ideal - quick test for interrupted ORFs in bacterial/microbial genomes☆15Jun 26, 2018Updated 7 years ago
- PopPUNK 👨🎤 (POPulation Partitioning Using Nucleotide Kmers)☆104Mar 2, 2026Updated last week
- VIGOR4☆21Aug 15, 2025Updated 6 months ago
- In silico prediction of E. coli serotype, pathotype and shiga toxin subtyping☆65Jun 5, 2025Updated 9 months ago
- A streamlined workflow and GUI for real-time species identification and pathogen characterization via nanopore sequencing data. Engineere…☆20Oct 4, 2024Updated last year
- Genome size estimation from long read overlaps☆81Mar 2, 2026Updated last week
- Mandrake 🌿/👨🔬🦆 – Fast visualisation of the population structure of pathogens using Stochastic Cluster Embedding☆39Mar 7, 2025Updated last year
- The Genomic Epidemiology Application Ontology describes the genomics, laboratory, clinical and epidemiological contextual information req…☆24Updated this week
- Introduction to Nanopore Sequencing - Prac material and presentations from The Omics Australia Tutorials Sydney (TOAST) workshop 19th - 2…☆10Jan 12, 2019Updated 7 years ago
- TAXnomic Profile Aggregation and STAndardisation☆42Nov 18, 2025Updated 3 months ago
- Renames headers in FASTA file☆12Jun 28, 2017Updated 8 years ago