Assembly of Nanopore Sequencing
☆17Jan 8, 2026Updated 2 months ago
Alternatives and similar repositories for Donut_Falls
Users that are interested in Donut_Falls are comparing it to the libraries listed below
Sorting:
- UPHL's Reference Free Pipeline☆27Updated this week
- Reference-based consensus creation☆59Feb 10, 2026Updated 3 weeks ago
- Spriggan is a pipeline used for assembly of bacterial whole genome sequence data and identification of antibiotic resistance genes.☆16Updated this week
- MycoSNP: Whole Genome Sequencing Analysis of Fungal Isolates☆89Feb 5, 2026Updated last month
- Python Toolkit for using containerized programs in either Singularity or Docker☆29Mar 19, 2024Updated last year
- A methodology to rapidly leverage whole genome sequencing of bacterial isolates for clinical identification.☆35Dec 2, 2024Updated last year
- A Nextflow pipeline for viral genomics (Influenza/RSV) supporting Illumina and Nanopore sequencing of clinical and wastewater samples.☆10Feb 27, 2026Updated last week
- Bioinformatics workflows for genomic characterization, submission preparation, and genomic epidemiology of pathogens of public health con…☆61Feb 27, 2026Updated last week
- ☆18Feb 25, 2026Updated last week
- A pipeline based on EMU, a taxonomic profiler optimized for long 16S rRNA reads.☆19Feb 27, 2026Updated last week
- Intra-species bacterial contamination detection☆25Feb 5, 2026Updated last month
- emm Automatic Isolate Labeller☆12Mar 25, 2025Updated 11 months ago
- tool to determine optimal refrerence genome given a set of fasta files☆15May 18, 2023Updated 2 years ago
- REcombination BARcode detector.☆16Apr 2, 2024Updated last year
- Predict MLST directly from uncorrected long reads☆27Oct 31, 2025Updated 4 months ago
- Stitch together Nanopore tiled amplicon data without polishing a reference☆17Jan 29, 2024Updated 2 years ago
- Real-time analysis pipeline for nanopore 16S rRNA data☆15Nov 29, 2022Updated 3 years ago
- CFSAN Shigella Typing Pipeline☆15Jul 6, 2023Updated 2 years ago
- A simple pipeline for bacterial assembly and quality control☆16Feb 26, 2026Updated last week
- 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
- StxTyper uses a standardized algorithm to accurately type both known and unknown Shiga toxin operons from assembled genomic sequence.☆17Dec 9, 2025Updated 2 months ago
- TaxTriage is a Nextflow workflow designed to agnostically identify and classify microbial organisms within short- or long-read metagenomi…☆62Updated this week
- MutTui pipeline to reconstruct mutational spectra for bacterial and viral datasets☆33Jul 2, 2024Updated last year
- 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
- Ultrafast sequence typing and gene detection from NGS raw reads☆20Apr 15, 2021Updated 4 years ago
- VIGOR4☆21Aug 15, 2025Updated 6 months ago
- SeqSero2☆39Oct 1, 2025Updated 5 months ago
- A simple nextflow pipeline for running kraken2 and bracken in a docker container☆20Oct 8, 2025Updated 4 months ago
- A pipeline for high-quality bacterial genome construction using ONT sequencing☆38Sep 22, 2022Updated 3 years ago
- Rapid identification of Staphylococcus aureus agr locus type and agr operon variants.☆10Jan 6, 2023Updated 3 years ago
- Automated Pipeline to Generate FTP Files and Manage Submission of Sequence Data to Public Repositories☆38Feb 20, 2026Updated 2 weeks ago
- TAXnomic Profile Aggregation and STAndardisation☆42Nov 18, 2025Updated 3 months ago
- rapid serotyping of Vibrio parahaemolyticus from whole genome sequencing data using serogroup-specific genes☆10Sep 2, 2021Updated 4 years ago
- The repository contains the source code of the NanoForms server (Czmil et al. NanoForms: an integrated server for processing, analysis an…☆11Feb 22, 2023Updated 3 years ago
- Dockerfiles and documentation on tools for public health bioinformatics☆221Updated this week
- Bioinformatics workflows for genomic characterization, submission preparation, and genomic epidemiology of viral pathogens of concern, es…☆42Aug 5, 2024Updated last year
- Interpretative standards for AMR genotypes☆27Updated this week
- Bacterial surveillance pipeline.☆27Dec 30, 2025Updated 2 months ago
- Assemble bacterial isolate genomes from Nanopore reads☆128Jan 22, 2025Updated last year