Influenza genome analysis Nextflow workflow
☆24Mar 10, 2026Updated 2 weeks ago
Alternatives and similar repositories for nf-flu
Users that are interested in nf-flu are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- A Nextflow pipeline for viral genomics (Influenza/RSV) supporting Illumina and Nanopore sequencing of clinical and wastewater samples.☆10Feb 27, 2026Updated 3 weeks ago
- Files and methodology pertaining to the sequencing and analysis of SARS-CoV-2, causative agent of COVID-19.☆32Mar 17, 2026Updated last week
- Organism-specific interpretation of AMR genotypes☆15Mar 17, 2026Updated last week
- ☆27Aug 2, 2023Updated 2 years ago
- Mycobacterium tuberculosis genomic analysis from Nanopore sequencing data☆14Jun 12, 2024Updated last year
- Experimental plugin to integrate GPT like prompt into Nextflow☆17Apr 15, 2024Updated last year
- A repo with just adapter sequences☆15Jul 7, 2025Updated 8 months ago
- Parallelised and automated construction of metagenomic classifier databases of different tools☆20Feb 20, 2026Updated last month
- Bacterial surveillance pipeline.☆27Dec 30, 2025Updated 2 months ago
- Surveillance of pathogens using population genomics and sequencing☆59Feb 13, 2026Updated last month
- A pipeline to identify (and remove) certain sequences from raw genomic data. Default taxon to identify (and remove) is Homo sapiens. Remo…☆24Nov 20, 2025Updated 4 months ago
- A simple pipeline for bacterial assembly and quality control☆16Updated this week
- whole genome MLST analysis☆51Mar 13, 2026Updated last week
- BACTpipe: An assembly and annotation pipeline for bacterial genomics☆20Dec 3, 2024Updated last year
- Bioinformatics Pipeline and Visualization resources☆65Aug 30, 2024Updated last year
- An `R` package for various phylogenetic and evolutionary biology data manipulations☆12Mar 5, 2018Updated 8 years ago
- Automated Pipeline to Generate FTP Files and Manage Submission of Sequence Data to Public Repositories☆39Feb 20, 2026Updated last month
- Mapping NCBI Genbank accession to GTDB accession☆14Feb 13, 2021Updated 5 years ago
- Benchmarking different ways of doing read (taxonomic) classification, with a focus on removal of contamination and MTB classification☆14Apr 8, 2024Updated last year
- Bioinformatics workflows for genomic characterization, submission preparation, and genomic epidemiology of viral pathogens of concern, es…☆42Aug 5, 2024Updated last year
- GRIMER performs analysis of microbiome studies and generates a portable and interactive dashboard integrating annotation, taxonomy and me…☆24Feb 6, 2023Updated 3 years ago
- Umbrella documentation project for Nextstrain☆18Mar 17, 2026Updated last week
- Bacterial Genomics workflow for short(Illumina) and long-read (Oxford Nanopore) sequencing data☆12Feb 20, 2026Updated last month
- TAXnomic Profile Aggregation and STAndardisation☆42Nov 18, 2025Updated 4 months ago
- A surveillance-oriented tool to strengthen the linkage between pathogen genetic clusters and epidemiological data☆48Feb 20, 2026Updated last month
- An SRA tool that takes as input local fastq file from a clinical infection sample, identifies and removes any significant human read, and…☆53Jul 24, 2025Updated 8 months ago
- Comprehensive resistance detection from WGS data☆19Feb 1, 2026Updated last month
- Nextflow workflows to assign Salmonella serotype based on Genome similarity using MASH, SOURMASH and KMA.☆13Dec 24, 2025Updated 3 months ago
- Influenza genome analysis Nextflow workflow☆31Sep 15, 2025Updated 6 months ago
- Framework to benchmark algorithms when detecting germline copy number variations (CNVs) from NGS data☆14Dec 24, 2024Updated last year
- Benchmark datasets for WGS analysis of SARS-CoV-2. (https://peerj.com/articles/13821/)☆60Mar 23, 2023Updated 3 years ago
- An RNA virus strain-level identification tool for short reads.☆23Updated this week
- Rapid identification of Staphylococcus aureus agr locus type and agr operon variants.☆10Jan 6, 2023Updated 3 years ago
- CFSAN Shigella Typing Pipeline☆15Jul 6, 2023Updated 2 years ago
- ☆15Jun 2, 2021Updated 4 years ago
- MutTui pipeline to reconstruct mutational spectra for bacterial and viral datasets☆33Jul 2, 2024Updated last year
- A nf-core pipeline for untargeted whole genome reconstruction with iSNV detection from metagenomic samples.☆31Mar 13, 2026Updated last week
- rapid serotyping of Vibrio parahaemolyticus from whole genome sequencing data using serogroup-specific genes☆10Sep 2, 2021Updated 4 years ago
- viralComplete: BLAST-based viral completeness verification☆24Oct 4, 2021Updated 4 years ago