rpetit3 / pastyView external linksLinks
A tool easily taken advantage of for in silico serogrouping of Pseudomonas aeruginosa isolates
☆13Aug 26, 2024Updated last year
Alternatives and similar repositories for pasty
Users that are interested in pasty are comparing it to the libraries listed below
Sorting:
- Spriggan is a pipeline used for assembly of bacterial whole genome sequence data and identification of antibiotic resistance genes.☆16Jan 23, 2026Updated 3 weeks ago
- Automated Pipeline to Generate FTP Files and Manage Submission of Sequence Data to Public Repositories☆38Jan 21, 2026Updated 3 weeks ago
- Finding regions of similarity between plasmids☆17Nov 2, 2022Updated 3 years ago
- ☆26Aug 2, 2023Updated 2 years ago
- Visualisation application for Klebsiella genotypes generated by Kleborate.☆10Sep 27, 2025Updated 4 months ago
- A random forest classifier to identify contigs of plasmid origin in contig and scaffold genomes☆20Apr 20, 2023Updated 2 years ago
- A pipeline for running AMRfinderPlus and collating results into functional classes☆91Dec 3, 2025Updated 2 months ago
- Targeted Detection and Reconstruction of Plasmids☆22May 7, 2024Updated last year
- The MLST pipeline developed by the PathOGiST research group☆36Nov 29, 2023Updated 2 years ago
- Docker containers for bioinformatics with a small footprint☆23Dec 18, 2025Updated last month
- hAMRoaster is an analysis pipeline that can compare the output of tools for detecting AMR genes and provide metrics of their performance☆22Mar 8, 2024Updated last year
- A pipeline for high-quality bacterial genome construction using ONT sequencing☆38Sep 22, 2022Updated 3 years ago
- Intra-species bacterial contamination detection☆25Feb 5, 2026Updated last week
- A taxonomic classifier of plasmids☆28Jul 7, 2021Updated 4 years ago
- Predict plasmids from uncorrected long read data☆41Oct 31, 2025Updated 3 months ago
- Experiments with using BIGSI data structure for metagenomic and QC applications☆19Aug 12, 2024Updated last year
- Plasmid and antimicrobial resistance pipeline☆16Dec 30, 2024Updated last year
- a comparative genome browser for bacteriophages☆20Jan 17, 2025Updated last year
- Recombination-free trees☆63Sep 1, 2025Updated 5 months ago
- k-mer based Pipeline to identify the Serotype from Illumina NGS reads☆26Jul 13, 2023Updated 2 years ago
- An R package identifying horizontal gene co-transfer between bacteria using association analysis and whole-genome sequences☆27Aug 8, 2022Updated 3 years ago
- Organism-specific interpretation of AMR genotypes☆15Mar 13, 2024Updated last year
- A pipeline for bioinformatics analysis of bacterial genomes☆32Updated this week
- Output FASTQ summary statistics in JSON format☆29Oct 30, 2022Updated 3 years ago
- CFSAN Shigella Typing Pipeline☆15Jul 6, 2023Updated 2 years ago
- Prophage Tracer: precisely tracing prophages in prokaryotic genomes using overlapping split-read alignment☆24Oct 16, 2024Updated last year
- A curated database of completed assemblies with taxonomy IDs☆48Feb 6, 2026Updated last week
- Bacterial genomes finishing tool for structural insights on draft genomes☆23Sep 22, 2023Updated 2 years ago
- ganon2 classifies genomic sequences against large sets of references efficiently, with integrated download and update of databases (refse…☆103Feb 5, 2026Updated last week
- ☆36Nov 11, 2022Updated 3 years ago
- A toolbox for pangenome analysis and threshold evaluation.☆99Jul 8, 2022Updated 3 years ago
- A mapping-based pipeline for creating a phylogeny from bacterial whole genome sequences☆62Nov 20, 2025Updated 2 months ago
- Benchmark datasets for WGS analysis of SARS-CoV-2. (https://peerj.com/articles/13821/)☆59Mar 23, 2023Updated 2 years ago
- VIGOR4☆21Aug 15, 2025Updated 5 months ago
- A hybrid assembly and MAG recovery pipeline (and more!)☆104Jan 27, 2026Updated 2 weeks ago
- Neural Bacteriocin Identifier - a recurrent neural network based software to predict bacteriocins from protein sequences.☆18Mar 25, 2023Updated 2 years ago
- PlasX, a machine learning classifier for identifying plasmid sequences based on genetic architecture☆40Feb 9, 2022Updated 4 years ago
- Growth Rate Index (GRiD) measures bacterial growth rate from reference genomes (including draft quality genomes) and metagenomic bins at …☆32May 22, 2020Updated 5 years ago
- FishTaco (Functional Shifts Taxonomic Contributors) is a metagenomic computational framework that aims to identify the driver taxa of mic…☆24Jul 3, 2021Updated 4 years ago