Fast k-mer based tool for multi locus sequence typing (MLST)
☆46Sep 3, 2020Updated 5 years ago
Alternatives and similar repositories for stringMLST
Users that are interested in stringMLST are comparing it to the libraries listed below
Sorting:
- Ultrafast sequence typing and gene detection from NGS raw reads☆20Apr 15, 2021Updated 4 years ago
- ☆16Oct 2, 2019Updated 6 years ago
- ☆23Feb 12, 2026Updated last month
- In silico taxonomic classification of Bacillus cereus group genomes using whole-genome sequencing data☆22May 8, 2024Updated last year
- Pipeline to generate NGS reads from a phylogeny☆39Sep 13, 2022Updated 3 years ago
- Genomic neighbor typing of bacterial pathogens using MinHash☆42Jan 10, 2023Updated 3 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
- (Obsolete) NCBI Prokaryotic Genome Annotation Pipeline. New site:☆16Sep 7, 2018Updated 7 years ago
- Generate mutated sequence files from a reference genome.☆11Dec 26, 2022Updated 3 years ago
- Software for article "Deep learning to predict the lab-of-origin of engineered DNA"☆13Aug 7, 2018Updated 7 years ago
- Assembly of Nanopore Sequencing☆17Jan 8, 2026Updated 2 months ago
- "Reads to report" for public health and clinical microbiology☆143Dec 9, 2025Updated 3 months ago
- Pipeline for analysing intergenic regions in bacteria☆39Oct 25, 2019Updated 6 years ago
- Bacterial Isolate Genome Sequence Database (BIGSdb): A platform for gene-by-gene bacterial population annotation and analysis.☆75Mar 9, 2026Updated last week
- Predict MLST directly from uncorrected long reads☆27Oct 31, 2025Updated 4 months ago
- Multilocus sequence typing by blast using the schemes from PubMLST☆30Jun 23, 2022Updated 3 years ago
- Northern Arizona SNP Pipeline☆20Oct 29, 2024Updated last year
- ⚡♠️ Assemble bacterial isolate genomes from Illumina paired-end reads☆257Dec 13, 2025Updated 3 months ago
- ⚡️🧬 FastMLST: A multi-core tool for multilocus sequence typing of draft genome assemblies☆25Nov 19, 2025Updated 4 months ago
- Paint genomes with taxa-specific k-mer probabilities☆15Apr 4, 2022Updated 3 years ago
- ☆16Mar 11, 2024Updated 2 years ago
- Mass screening of contigs for antimicrobial and virulence genes☆482Jan 31, 2026Updated last month
- NCBI Pathogen Detection Portal toolkit☆11Sep 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
- Homebrew formulae for bioinformatics software only available for Linux☆27Aug 23, 2019Updated 6 years ago
- Reorients assembled microbial sequences☆136Aug 21, 2025Updated 6 months ago
- BACTpipe: An assembly and annotation pipeline for bacterial genomics☆20Dec 3, 2024Updated last year
- Scan contig files against PubMLST typing schemes☆269Jan 2, 2026Updated 2 months ago
- Private, browser-based placement of genome sequences on phylogenetic trees using UShER.☆11Nov 22, 2024Updated last year
- Short Read Sequence Typing for Bacterial Pathogens☆145Jun 20, 2021Updated 4 years ago
- RCandy: an R package for visualising homologous recombination events in bacterial genomes☆25Jun 17, 2022Updated 3 years ago
- Animated GIF of flow cell performance from sequencing summary file.☆13Feb 20, 2018Updated 8 years ago
- Standalone Python re-implementation of the POLCA polisher from MaSuRCA☆44Aug 20, 2025Updated 7 months ago
- CFSAN Shigella Typing Pipeline☆15Jul 6, 2023Updated 2 years ago
- Bayesian inference of ancestral dates on bacterial phylogenetic trees☆97Dec 9, 2025Updated 3 months ago
- Plasmid and antimicrobial resistance pipeline☆16Dec 30, 2024Updated last year
- Output FASTQ summary statistics in JSON format☆29Oct 30, 2022Updated 3 years ago
- Automated Pipeline to Generate FTP Files and Manage Submission of Sequence Data to Public Repositories☆39Feb 20, 2026Updated last month
- Nextflow workflows to assign Salmonella serotype based on Genome similarity using MASH, SOURMASH and KMA.☆13Dec 24, 2025Updated 2 months ago