viral-ngs: complete pipelines
☆73Feb 27, 2026Updated last week
Alternatives and similar repositories for viral-pipelines
Users that are interested in viral-pipelines are comparing it to the libraries listed below
Sorting:
- Experiments with using BIGSI data structure for metagenomic and QC applications☆19Aug 12, 2024Updated last year
- Bioinformatics workflows for genomic characterization, submission preparation, and genomic epidemiology of viral pathogens of concern, es…☆42Aug 5, 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
- ☆21Jan 23, 2026Updated last month
- Bioinformatics workflows for genomic characterization, submission preparation, and genomic epidemiology of pathogens of public health con…☆61Updated this week
- k-mer based Pipeline to identify the Serotype from Illumina NGS reads☆25Jul 13, 2023Updated 2 years ago
- VIGOR4☆21Aug 15, 2025Updated 6 months ago
- A tool easily taken advantage of for in silico serogrouping of Pseudomonas aeruginosa isolates☆13Aug 26, 2024Updated last year
- Workflow Description Language developer tools & local runner☆200Feb 8, 2026Updated last month
- PiGx SARS-CoV-2 wastewater sequencing pipeline☆18May 3, 2023Updated 2 years ago
- ☆27Aug 2, 2023Updated 2 years ago
- SARS-CoV-2: detecting recombinations in viruses using large data sets with high sequence similarity☆13Aug 14, 2023Updated 2 years ago
- Rich IDE support for Workflow Description Language☆43Mar 28, 2025Updated 11 months ago
- Portable WDL workflows for CZ ID production pipelines☆51Jun 17, 2025Updated 8 months ago
- Database of virus RdRP barcode sequences☆16Jul 5, 2024Updated last year
- An open-source pathogen sequence database dedicated to equitable sharing, transparent governance, & empowering global public health.☆51Updated this week
- viral-ngs: command line tools and wrappers for processing raw viral genomic data☆194Feb 25, 2026Updated last week
- An SRA tool that takes as input local fastq file from a clinical infection sample, identifies and removes any significant human read, and…☆52Jul 24, 2025Updated 7 months ago
- Detecting recombination of viral lineages☆11Dec 23, 2025Updated 2 months ago
- Nextflow workflows to assign Salmonella serotype based on Genome similarity using MASH, SOURMASH and KMA.☆13Dec 24, 2025Updated 2 months ago
- R Data Exploration for Serratus☆15Mar 29, 2023Updated 2 years ago
- IRMA (the Iterative Refinement Meta-Assembler) is a highly configurable and adaptive tool for virus genome assembly.☆23Dec 19, 2025Updated 2 months ago
- Metagenomic Intra-Species Diversity Analysis (MIDAS)☆42Sep 3, 2024Updated last year
- Official place for proposals and details around monkeypox virus lineage designations☆23Dec 9, 2025Updated 3 months ago
- Nextflow workflow template repository☆20Dec 15, 2025Updated 2 months ago
- Create WDL documentation using Markdown.☆28Nov 25, 2025Updated 3 months ago
- Viral genome alignment, mutation calling, clade assignment, quality checks and phylogenetic placement☆252Updated this week
- ☆15May 22, 2025Updated 9 months ago
- A versatile toolkit for k-mers with taxonomic information☆82Aug 28, 2025Updated 6 months ago
- Assembly and binning of metagenomes☆275Updated this week
- Prepares a SARS-CoV-2 submission for GISAID, NCBI or ENA. Can read GISAID or NCBI files, or plain fasta+tsv/csv/xls. Finds files in input…☆36May 1, 2022Updated 3 years ago
- Viral Annotation DefineR: classification and annotation of viral sequences based on RefSeq annotation☆114Updated this week
- TreeKnit is a package that infers Ancestral Reassortment Graphs for segmented genomes (typically, human influenza).☆14Feb 18, 2025Updated last year
- This is a simple introductory tutorial to help you get started with using BEAST2 and its accomplices.☆11Jul 8, 2025Updated 8 months ago
- Frankies Scalable, AI-Based Antibody Design Pipeline☆18Feb 20, 2026Updated 2 weeks ago
- VirID: An integrated platform for the discovery and characterization of RNA Viruses☆23Jan 8, 2026Updated 2 months ago
- ☆18Mar 5, 2017Updated 9 years ago
- The Genomic Epidemiology Application Ontology describes the genomics, laboratory, clinical and epidemiological contextual information req…☆24Updated this week
- Bacterial surveillance pipeline.☆27Dec 30, 2025Updated 2 months ago