whole genome MLST analysis
☆55Jun 17, 2026Updated 2 months ago
Alternatives and similar repositories for pyMLST
Users that are interested in pyMLST are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Pipeline detecting distant and putative novel insertion sequences in prokaryotic genomes☆13Jun 10, 2021Updated 5 years ago
- rapid serotyping of Vibrio parahaemolyticus from whole genome sequencing data using serogroup-specific genes☆10Sep 2, 2021Updated 4 years ago
- A taxonomic classifier of plasmids☆29Jul 7, 2021Updated 5 years ago
- Finding regions of similarity between plasmids☆17Jul 15, 2026Updated last month
- Visualisation application for Klebsiella genotypes generated by Kleborate.☆10Mar 10, 2026Updated 5 months ago
- Managed Database hosting by DigitalOcean • AdPostgreSQL, MySQL, MongoDB, Kafka, Valkey, and OpenSearch available. Automatically scale up storage and focus on building your apps.
- ⚡️🧬 FastMLST: A multi-core tool for multilocus sequence typing of draft genome assemblies☆26Jul 10, 2026Updated last month
- ☆27Aug 2, 2023Updated 3 years ago
- Targeted Detection and Reconstruction of Plasmids☆22May 7, 2024Updated 2 years ago
- In silico prediction of E. coli serotype, pathotype and shiga toxin subtyping☆66Jun 5, 2025Updated last year
- A pipeline for running AMRfinderPlus and collating results into functional classes☆102Updated this week
- tool to determine optimal refrerence genome given a set of fasta files☆15May 18, 2023Updated 3 years ago
- Experiments with using BIGSI data structure for metagenomic and QC applications☆19Aug 12, 2024Updated 2 years ago
- Ultrafast sequence typing and gene detection from NGS raw reads☆20Apr 15, 2021Updated 5 years ago
- hAMRoaster is an analysis pipeline that can compare the output of tools for detecting AMR genes and provide metrics of their performance☆23Mar 8, 2024Updated 2 years ago
- Wordpress hosting with auto-scaling - Free Trial Offer • AdFully Managed hosting for WordPress and WooCommerce businesses that need reliable, auto-scalable performance. Cloudways SafeUpdates now available.
- A surveillance-oriented tool to strengthen the linkage between pathogen genetic clusters and epidemiological data☆50Feb 20, 2026Updated 6 months ago
- Dryad is a Nextflow pipeline for examining prokaryote relatedness. Dryad can perform a reference free analysis and/or SNP analysis.☆21Aug 17, 2026Updated last week
- A simple pipeline for bacterial assembly and quality control☆16Aug 12, 2026Updated 2 weeks ago
- The MLST pipeline developed by the PathOGiST research group☆39Nov 29, 2023Updated 2 years ago
- The Whole Genome Sequencing Coverage Plot (wgscovplot) is a tool to generate HTML Interactive Coverage Plot given coverage depth informat…☆19May 3, 2024Updated 2 years ago
- Host depletion optimised for clinical metagenomic sequencing applications☆19Jul 9, 2026Updated last month
- A pipeline for bioinformatics analysis of bacterial genomes☆34Jul 17, 2026Updated last month
- Hybrid Assembler for Plasmids☆10Jul 28, 2022Updated 4 years ago
- software to identify primers that can distinguish genomes☆20Jan 23, 2026Updated 7 months ago
- Managed hosting for WordPress and PHP on Cloudways • AdManaged hosting for WordPress, Magento, Laravel, or PHP apps, on multiple cloud providers. Deploy in minutes on Cloudways by DigitalOcean.
- A Python package to update the MLST database for the mlst tool.☆31Jul 22, 2026Updated last month
- Automated Pipeline to Generate FTP Files and Manage Submission of Sequence Data to Public Repositories☆41Aug 11, 2026Updated 2 weeks ago
- Multi-platform genome assembly pipeline for Illumina, Nanopore and PacBio reads☆66Jan 22, 2026Updated 7 months ago
- Predicting plasmid contigs from assemblies using single copy marker genes, plasmid genes, kmers - Developed by Linda van der Graaf☆50May 18, 2026Updated 3 months ago
- A simple script to run an alignment with nucmer and visualise its results.☆10Apr 17, 2023Updated 3 years ago
- Parse multiple Antimicrobial Resistance Analysis Reports into a common data structure☆182Aug 10, 2026Updated 2 weeks ago
- MOB-suite: Software tools for clustering, reconstruction and typing of plasmids from draft assemblies☆182Apr 16, 2025Updated last year
- snakemake-powered cli to download genomes using NCBI datasets☆15Aug 14, 2025Updated last year
- Assign genotypes to Salmonella Typhi genomes based on VCF files (mapped to Typhi CT18 reference genome)☆30Jul 18, 2025Updated 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.
- detect temperate phage (active prophage) in assembled bacterial genome sequences☆15Feb 10, 2022Updated 4 years ago
- PlasmidID is a mapping-based, assembly-assisted plasmid identification tool that analyzes and gives graphic solution for plasmid identifi…☆44Jul 23, 2021Updated 5 years ago
- An accurate and sensitive bacterial plasmid identification tool based on deep machine-learning of shared k-mers and genomic features.☆50Apr 20, 2023Updated 3 years ago
- Generic but comprehensive pipeline for prokaryotic genome annotation and interrogation with interactive reports and shiny app.☆110Jan 22, 2026Updated 7 months ago
- A pipeline for high-quality bacterial genome construction using ONT sequencing☆40Sep 22, 2022Updated 3 years ago
- Scans genome contigs against the ResFinder, PlasmidFinder, and PointFinder databases.☆206Jun 10, 2026Updated 2 months ago
- Melon: metagenomic long-read-based taxonomic identification and quantification using marker genes☆38Jun 4, 2026Updated 2 months ago