epi2me-labs / wf-fluView external linksLinks
☆21Jan 23, 2026Updated 3 weeks ago
Alternatives and similar repositories for wf-flu
Users that are interested in wf-flu are comparing it to the libraries listed below
Sorting:
- Influenza genome analysis Nextflow workflow☆31Sep 15, 2025Updated 5 months ago
- VIGOR4☆21Aug 15, 2025Updated 6 months ago
- SARS-CoV-2: detecting recombinations in viruses using large data sets with high sequence similarity☆13Aug 14, 2023Updated 2 years ago
- Repo for PrimerSchemes☆17Dec 18, 2025Updated last month
- For all your cluster needs☆17Feb 3, 2023Updated 3 years ago
- Nextflow workflows to assign Salmonella serotype based on Genome similarity using MASH, SOURMASH and KMA.☆13Dec 24, 2025Updated last month
- CFSAN Shigella Typing Pipeline☆15Jul 6, 2023Updated 2 years ago
- Rapid identification of Staphylococcus aureus agr locus type and agr operon variants.☆10Jan 6, 2023Updated 3 years ago
- ☆10Apr 16, 2025Updated 9 months ago
- Cluster informed Shigella and EIEC serotyping tool from Illumina reads and assemblies☆12Jun 30, 2023Updated 2 years ago
- Influenza data pipeline to automate genotyping assignment☆39Oct 14, 2025Updated 4 months ago
- A simple nextflow pipeline for running kraken2 and bracken in a docker container☆20Oct 8, 2025Updated 4 months ago
- INSaFLU-TELEVIR: an free web-based (but also locally installable) bioinformatics suite for virus metagenomic detection and routine genomi…☆41Updated this week
- Mycobacterium tuberculosis genomic analysis from Nanopore sequencing data☆13Jun 12, 2024Updated last year
- Archived - please see updated sccmec tool at link below☆13Aug 30, 2024Updated last year
- Quasitools is a collection of tools for analysing viral quasispecies data.☆27Nov 25, 2021Updated 4 years ago
- emm Automatic Isolate Labeller☆12Mar 25, 2025Updated 10 months ago
- Assign genotypes to Salmonella Typhi genomes based on VCF files (mapped to Typhi CT18 reference genome)☆28Jul 18, 2025Updated 6 months ago
- A pipeline for comprehensive genomic analyses of Mycobacterium tuberculosis with a focus on clinical decision making as well as research☆19Jan 8, 2026Updated last month
- SARs-CoV-2 Primer schemes☆16May 14, 2025Updated 9 months ago
- ☆14Jun 30, 2021Updated 4 years ago
- Predict MLST directly from uncorrected long reads☆27Oct 31, 2025Updated 3 months ago
- Organism-specific interpretation of AMR genotypes☆15Mar 13, 2024Updated last year
- Stitch together Nanopore tiled amplicon data without polishing a reference☆17Jan 29, 2024Updated 2 years ago
- Bioinformatics workflows for genomic characterization, submission preparation, and genomic epidemiology of pathogens of public health con…☆60Updated this week
- ☆26Aug 2, 2023Updated 2 years ago
- 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
- Real-time analysis pipeline for nanopore 16S rRNA data☆15Nov 29, 2022Updated 3 years ago
- Pneumococcal Capsular Typing tool for NGS data☆18Apr 6, 2021Updated 4 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 last year
- A simple pipeline for bacterial assembly and quality control☆16Jan 30, 2026Updated 2 weeks ago
- TaxTriage is a Nextflow workflow designed to agnostically identify and classify microbial organisms within short- or long-read metagenomi…☆62Updated this week
- Pipeline for processing FASTQ data from an Illumina MiSeq to genotype human RNA viruses like HIV and hepatitis C☆19Updated this week
- Official place for proposals and details around monkeypox virus lineage designations☆23Dec 9, 2025Updated 2 months ago
- An SRA tool that takes as input local fastq file from a clinical infection sample, identifies and removes any significant human read, and…☆51Jul 24, 2025Updated 6 months ago
- Olivar: towards automated variant aware primer design for multiplex tiled amplicon sequencing of pathogens☆37Jan 22, 2026Updated 3 weeks ago
- catalog for long-read sequencing tools☆32Feb 14, 2023Updated 3 years ago
- Influenza genome analysis Nextflow workflow☆24Jan 26, 2026Updated 2 weeks ago
- MTBseq is an automated pipeline for mapping, variant calling and detection of resistance mediating and phylogenetic variants from illumin…☆47Sep 8, 2025Updated 5 months ago