whole genome MLST analysis
☆51Mar 13, 2026Updated last week
Alternatives and similar repositories for pyMLST
Users that are interested in pyMLST are comparing it to the libraries listed below
Sorting:
- Pipeline detecting distant and putative novel insertion sequences in prokaryotic genomes☆13Jun 10, 2021Updated 4 years ago
- A taxonomic classifier of plasmids☆28Jul 7, 2021Updated 4 years ago
- rapid serotyping of Vibrio parahaemolyticus from whole genome sequencing data using serogroup-specific genes☆10Sep 2, 2021Updated 4 years ago
- Finding regions of similarity between plasmids☆17Nov 2, 2022Updated 3 years ago
- ⚡️🧬 FastMLST: A multi-core tool for multilocus sequence typing of draft genome assemblies☆25Nov 19, 2025Updated 4 months ago
- ☆27Aug 2, 2023Updated 2 years ago
- Organism-specific interpretation of AMR genotypes☆15Mar 13, 2024Updated 2 years ago
- Targeted Detection and Reconstruction of Plasmids☆22May 7, 2024Updated last year
- In silico prediction of E. coli serotype, pathotype and shiga toxin subtyping☆65Jun 5, 2025Updated 9 months ago
- A pipeline for running AMRfinderPlus and collating results into functional classes☆91Updated this week
- tool to determine optimal refrerence genome given a set of fasta files☆15May 18, 2023Updated 2 years ago
- 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 2 years ago
- Ultrafast sequence typing and gene detection from NGS raw reads☆20Apr 15, 2021Updated 4 years ago
- Dryad is a Nextflow pipeline for examining prokaryote relatedness. Dryad can perform a reference free analysis and/or SNP analysis.☆18Updated this week
- A simple pipeline for bacterial assembly and quality control☆16Mar 12, 2026Updated last week
- A surveillance-oriented tool to strengthen the linkage between pathogen genetic clusters and epidemiological data☆48Feb 20, 2026Updated last month
- ☆29Mar 5, 2026Updated 2 weeks ago
- The Whole Genome Sequencing Coverage Plot (wgscovplot) is a tool to generate HTML Interactive Coverage Plot given coverage depth informat…☆19May 3, 2024Updated last year
- A pipeline for bioinformatics analysis of bacterial genomes☆32Updated this week
- The MLST pipeline developed by the PathOGiST research group☆36Nov 29, 2023Updated 2 years ago
- Automated Pipeline to Generate FTP Files and Manage Submission of Sequence Data to Public Repositories☆39Feb 20, 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
- Experiments with using BIGSI data structure for metagenomic and QC applications☆19Aug 12, 2024Updated last year
- Rapidly extract reads from a FASTQ file based on taxonomic classification via Kraken2.☆13Jan 26, 2026Updated last month
- Multi-platform genome assembly pipeline for Illumina, Nanopore and PacBio reads☆64Jan 22, 2026Updated last month
- software to identify primers that can distinguish genomes☆20Jan 23, 2026Updated last month
- Parse multiple Antimicrobial Resistance Analysis Reports into a common data structure☆175Feb 26, 2026Updated 3 weeks ago
- snakemake-powered cli to download genomes using NCBI datasets☆14Aug 14, 2025Updated 7 months ago
- MOB-suite: Software tools for clustering, reconstruction and typing of plasmids from draft assemblies☆171Apr 16, 2025Updated 11 months ago
- Scans genome contigs against the ResFinder, PlasmidFinder, and PointFinder databases.☆191Mar 6, 2026Updated 2 weeks ago
- An accurate and sensitive bacterial plasmid identification tool based on deep machine-learning of shared k-mers and genomic features.☆49Apr 20, 2023Updated 2 years ago
- detect temperate phage (active prophage) in assembled bacterial genome sequences☆14Feb 10, 2022Updated 4 years ago
- A pipeline for high-quality bacterial genome construction using ONT sequencing☆38Sep 22, 2022Updated 3 years ago
- Generic but comprehensive pipeline for prokaryotic genome annotation and interrogation with interactive reports and shiny app.☆106Jan 22, 2026Updated last month
- Mass screening of contigs for antimicrobial and virulence genes☆482Jan 31, 2026Updated last month
- Melon: metagenomic long-read-based taxonomic identification and quantification using marker genes☆35Apr 26, 2025Updated 10 months ago
- PlasmidID is a mapping-based, assembly-assisted plasmid identification tool that analyzes and gives graphic solution for plasmid identifi…☆43Jul 23, 2021Updated 4 years ago
- Assign genotypes to Salmonella Typhi genomes based on VCF files (mapped to Typhi CT18 reference genome)☆29Jul 18, 2025Updated 8 months ago
- Predict plasmids from uncorrected long read data☆41Feb 27, 2026Updated 3 weeks ago