Influenza data pipeline to automate genotyping assignment
☆39Oct 14, 2025Updated 4 months ago
Alternatives and similar repositories for GenoFLU
Users that are interested in GenoFLU are comparing it to the libraries listed below
Sorting:
- FluMut is a command-line tool to find markers of interest in H5N1 avian influenza viruses.☆13Feb 3, 2026Updated last month
- CFSAN Shigella Typing Pipeline☆15Jul 6, 2023Updated 2 years ago
- ☆21Jan 23, 2026Updated last month
- emm Automatic Isolate Labeller☆12Mar 25, 2025Updated 11 months ago
- Extract subsets of ONT (Nanopore) reads based on time☆23Sep 12, 2024Updated last year
- TaxTriage is a Nextflow workflow designed to agnostically identify and classify microbial organisms within short- or long-read metagenomi…☆62Feb 25, 2026Updated last week
- Consensus sequences for U.S. H5N1 clade 2.3.4.4b☆37Feb 25, 2026Updated last week
- UPHL's Reference Free Pipeline☆27Updated this week
- IRMA (the Iterative Refinement Meta-Assembler) is a highly configurable and adaptive tool for virus genome assembly.☆23Dec 19, 2025Updated 2 months 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
- 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
- MycoSNP: Whole Genome Sequencing Analysis of Fungal Isolates☆89Feb 5, 2026Updated last month
- Rapid identification of Staphylococcus aureus agr locus type and agr operon variants.☆10Jan 6, 2023Updated 3 years ago
- Nextflow workflows to assign Salmonella serotype based on Genome similarity using MASH, SOURMASH and KMA.☆13Dec 24, 2025Updated 2 months ago
- Bioinformatics workflows for genomic characterization, submission preparation, and genomic epidemiology of viral pathogens of concern, es…☆42Aug 5, 2024Updated last year
- A methodology to rapidly leverage whole genome sequencing of bacterial isolates for clinical identification.☆35Dec 2, 2024Updated last year
- interactive barplot for amplicon sequencing☆13Dec 5, 2024Updated last year
- NCBI Pathogen Detection Portal toolkit☆11Sep 6, 2023Updated 2 years ago
- Cluster informed Shigella and EIEC serotyping tool from Illumina reads and assemblies☆12Jun 30, 2023Updated 2 years ago
- ☆10Apr 16, 2025Updated 10 months ago
- A microbial genomic analysis pipeline used by the Djordjevic Lab☆13Feb 9, 2025Updated last year
- ☆27Aug 2, 2023Updated 2 years ago
- VIGOR4☆21Aug 15, 2025Updated 6 months ago
- Bioinformatics workflows for genomic characterization, submission preparation, and genomic epidemiology of pathogens of public health con…☆61Updated this week
- ☆20Feb 12, 2026Updated 3 weeks ago
- A simple nextflow pipeline for running kraken2 and bracken in a docker container☆20Oct 8, 2025Updated 4 months ago
- ☆22Feb 2, 2026Updated last month
- Bacterial surveillance pipeline.☆27Dec 30, 2025Updated 2 months ago
- Phylogenetic maximum representation sampling: choosing most representative strains or taxa☆40Sep 23, 2025Updated 5 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…☆52Jul 24, 2025Updated 7 months ago
- Script that labels phylogenetic clades based on the clade of the nearest neighbor using patristic distances determined from the tree.☆15Dec 11, 2024Updated last year
- 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
- Ampseer examines reads in fastq format and identifies which multiplex PCR primer set was used to generate the SARS-CoV-2 sequencing libra…☆15Feb 27, 2024Updated 2 years ago
- Bioinformatics Pipeline and Visualization resources☆63Aug 30, 2024Updated last year
- Fast viral consensus genome reconstruction☆25Feb 5, 2026Updated 3 weeks ago
- Intra-species bacterial contamination detection☆25Feb 5, 2026Updated 3 weeks ago
- Automated Pipeline to Generate FTP Files and Manage Submission of Sequence Data to Public Repositories☆38Feb 20, 2026Updated last week
- VarSkip multiplex PCR designs for SARS-CoV-2 sequencing☆14Jun 14, 2022Updated 3 years ago