Ultrafast sequence typing and gene detection from NGS raw reads
☆20Apr 15, 2021Updated 4 years ago
Alternatives and similar repositories for STing
Users that are interested in STing are comparing it to the libraries listed below
Sorting:
- Predict MLST directly from uncorrected long reads☆27Oct 31, 2025Updated 4 months ago
- In silico taxonomic classification of Bacillus cereus group genomes using whole-genome sequencing data☆22May 8, 2024Updated last year
- A simple nextflow pipeline for running kraken2 and bracken in a docker container☆20Oct 8, 2025Updated 4 months ago
- Fast k-mer based tool for multi locus sequence typing (MLST)☆46Sep 3, 2020Updated 5 years ago
- Intra-species bacterial contamination detection☆25Feb 5, 2026Updated 3 weeks ago
- Nextflow workflows to assign Salmonella serotype based on Genome similarity using MASH, SOURMASH and KMA.☆13Dec 24, 2025Updated 2 months ago
- A simple pipeline for bacterial assembly and quality control☆16Feb 17, 2026Updated last week
- interactive barplot for amplicon sequencing☆13Dec 5, 2024Updated last year
- Files and methodology pertaining to the sequencing and analysis of SARS-CoV-2, causative agent of COVID-19.☆32Nov 19, 2025Updated 3 months ago
- BACTpipe: An assembly and annotation pipeline for bacterial genomics☆20Dec 3, 2024Updated last year
- whole genome MLST analysis☆51Updated this week
- The MLST pipeline developed by the PathOGiST research group☆36Nov 29, 2023Updated 2 years ago
- IRIDA Next☆13Updated this week
- List and download schemes from pubMLST.org and other BIGSDB servers☆10Oct 14, 2024Updated last year
- Mycobacterium tuberculosis genomic analysis from Nanopore sequencing data☆13Jun 12, 2024Updated last year
- ⚡️🧬 FastMLST: A multi-core tool for multilocus sequence typing of draft genome assemblies☆25Nov 19, 2025Updated 3 months ago
- A taxonomic classifier of plasmids☆28Jul 7, 2021Updated 4 years ago
- Genomic neighbor typing of bacterial pathogens using MinHash☆42Jan 10, 2023Updated 3 years ago
- Luslab nextflow modules☆14Apr 30, 2021Updated 4 years ago
- Assign genotypes to Salmonella Typhi genomes based on VCF files (mapped to Typhi CT18 reference genome)☆29Jul 18, 2025Updated 7 months ago
- Rapid determination of appropriate reference genomes.☆100Jan 22, 2025Updated last year
- ☆14Jun 30, 2021Updated 4 years ago
- Python Toolkit for using containerized programs in either Singularity or Docker☆29Mar 19, 2024Updated last year
- Variant call verification☆16May 12, 2025Updated 9 months ago
- Organism-specific interpretation of AMR genotypes☆15Mar 13, 2024Updated last year
- ☆27Aug 2, 2023Updated 2 years ago
- Output FASTQ summary statistics in JSON format☆29Oct 30, 2022Updated 3 years ago
- Real-time analysis pipeline for nanopore 16S rRNA data☆15Nov 29, 2022Updated 3 years ago
- Assembly of Nanopore Sequencing☆17Jan 8, 2026Updated last month
- CFSAN Shigella Typing Pipeline☆15Jul 6, 2023Updated 2 years ago
- Predicting Future Influenza Virus Sequences with Machine Learning☆31Feb 11, 2018Updated 8 years ago
- Get microbial sequence data easier and faster☆28Nov 7, 2019Updated 6 years ago
- MutTui pipeline to reconstruct mutational spectra for bacterial and viral datasets☆33Jul 2, 2024Updated last year
- A scalable bacterial genome assembly, annotation and analysis pipeline☆74Dec 5, 2023Updated 2 years ago
- Sequence-independent identification and removal of adapters/systemic contamination in shotgun sequencing data. https://doi.org/10.1093/bi…☆18Apr 4, 2023Updated 2 years ago
- A mapping-based pipeline for creating a phylogeny from bacterial whole genome sequences☆63Nov 20, 2025Updated 3 months ago
- ☆10Jan 20, 2022Updated 4 years ago
- Influenza genome analysis Nextflow workflow☆24Jan 26, 2026Updated last month
- ☆50Mar 11, 2022Updated 3 years ago