All Resources
Browse the complete collection of CDC Influenza Division resources, or use the navigation to filter by category.
2026-27 Influenza Season Surveillance Guidance
Surveillance guidance for the 2026-27 influenza season, covering monitoring of seasonal influenza viruses and detection of novel influenza A viruses, includi...
Epidemiology LaboratoryAutomated RNA Extraction using QIAcube HT
Standard operating procedure for automated RNA extraction using the QIAcube HT instrument for influenza and respiratory virus sample processing.
LaboratoryDNA Quantification with Qubit dsDNA High Sensitivity Kit
Procedure for quantifying double-stranded DNA using the Qubit fluorometer and the dsDNA High Sensitivity assay kit for quality control of sequencing libraries.
LaboratoryFlu Labs Genetic Data Portal
Secure CDC portal where State Public Health Laboratories retrieve the sequencing results for specimens they submitted to their National Influenza Reference C...
LaboratoryIRMA
IRMA (the Iterative Refinement Meta-Assembler) is a highly configurable and adaptive tool for virus genome assembly.
SoftwareInfluenza Bioinformatics Workshop
CDC bioinformatics workshop covering computer fundamentals, programming, environments and containers, genomics and analysis, phylogenetics and epi, quality a...
TrainingInfluenza Specimen Submission Form
Form for submitting influenza specimens to the CDC Influenza Division, capturing specimen, patient, and submitter information required for laboratory testing...
LaboratoryLimited-heft-of-weight-based-outcomes-in-predicting-influenza-A-virus-disease-severity-in-ferrets
Kieran et al. 2026 (PLoS Computational Biology) - R code for weight-based measurements in influenza-infected ferrets.
ZoonoticMIRA
MIRA: Portable, Interactive Application for High-Quality Influenza, SARS-CoV-2 and RSV Genome Assembly, Annotation, and Curation.
SoftwareMIRA-NF
Nextflow implementation of MIRA for scalable, high-quality influenza, SARS-CoV-2 and RSV genome assembly, annotation, and curation.
SoftwareMRT-PCR Purification using Exonuclease
Procedure for purifying MRT-PCR products using exonuclease treatment to remove residual primers and single-stranded DNA prior to library preparation.
LaboratoryMRT-PCR of Influenza A Viruses for Sequencing
Multi-segment reverse transcription PCR protocol for amplifying influenza A virus genome segments for sequencing. Current revision.
LaboratoryManual Procedure Illumina DNA Prep Library SOP
Manual procedure for Illumina DNA Prep library preparation, covering tagmentation, cleanup, and amplification steps for sequencing library construction. Curr...
LaboratoryMiSeq Library Loading Preparation
Standard operating procedure for preparing and loading sequencing libraries onto the Illumina MiSeq platform for influenza virus characterization.
LaboratoryMulti-segment Reverse Transcription-PCR (M-RTPCR) of Influenza A and B
Protocol for multi-segment reverse transcription PCR of both influenza A and influenza B viruses, generating full-genome amplicons for sequencing.
LaboratoryNative Library Prep & Nanopore Sequencing of InfA Virus & SARS-CoV-2 S-gene Amplicons
Protocol for native library preparation and Oxford Nanopore sequencing of influenza A virus and SARS-CoV-2 S-gene amplicons. Current revision.
LaboratoryPerforming a MiSeq Next Generation Sequencing Run
Standard operating procedure for setting up and performing a next generation sequencing run on the Illumina MiSeq platform.
LaboratoryPreparation of DNA Libraries and Loading on the MiSeq i100
Standard operating procedure for preparing DNA sequencing libraries and loading them onto the Illumina MiSeq i100 platform for influenza virus characterization.
LaboratoryPreparation of DNA Libraries and Loading on the NextSeq 1000/2000
Standard operating procedure for preparing DNA sequencing libraries and loading them onto the Illumina NextSeq 1000/2000 platform for influenza virus charact...
LaboratoryQIAxcel Sample Preparation and Quality Control Procedure
Procedure for preparing samples and performing quality control analysis using the QIAxcel capillary electrophoresis system for PCR product verification.
LaboratoryRT-PCR of the SARS-CoV-2 S-gene for Sequencing
Reverse transcription PCR protocol targeting the SARS-CoV-2 S-gene to generate amplicons for downstream sequencing applications.
LaboratorySeasonal Flu Sequence References
Curated GISAID EPI_SET genetic sequence references for seasonal influenza (H3N2, H1N1pdm09, B Victoria), including Complete and Contemporary per-segment data...
Datasetsam4N1Phylogenetics
Phylogenetic Analysis and Characterization of am4N1 Neuraminidases from North American A(H5N1) HPAI.
Zoonoticclassifying-influenza-trends
Code repository for published manuscript on classifying influenza hospitalization trends.
Epidemiologyclean-genes
A rust crate that automatically cleans up a gene alignment by trimming to ORF and identifying and/or removing problematic sequences.
Softwarecomparative-airborne-virus-shedding-with-diverse-influenza-strains-in-ferrets
Pulit-Penaloza et al. 2026 (Nature Communications) - R code advancing A(H5N1) influenza risk assessment in ferrets through comparative evaluation of airborne...
Zoonoticdais-ribosome
DAIS-ribosome annotates CDS and protein products for supported virus genomes into database-oriented output.
SoftwareeditMSA
A collection of scripts for editing and manipulating multiple sequence alignment files.
Softwareflu-antiviral-model
Modeling the potential impacts of outpatient antiviral treatment in reducing influenza-associated hospitalizations in the United States.
Epidemiologyflu-nursing-home-model
Influenza transmission and impact modeling in nursing home settings.
Epidemiologyhubhelpr
R package providing helper functions for CDC forecast hub maintenance and report generation.
Softwareifx-convert
A collection of low-dependency, bioinformatic format and data conversion scripts.
Softwareinfluenza-cluster-us
Understanding spatiotemporal clustering of seasonal influenza in the United States.
Epidemiologyinfluenza-generation_time-us
Estimating the generation time for influenza transmission using household data in the United States.
Epidemiologymachine-learning-influenza-ferret-model
Kieran et al. 2024 - Communication Biology - R code for machine learning in influenza infected ferrets.
Zoonoticmachine-learning-influenza-lethality-ferret
Kieran et al. 2025 (Scientific Reports) - R code for lethality/morbidity machine learning with tissues in influenza-infected ferrets.
Zoonoticmachine-learning-influenza-transmission-ferret
Kieran et al. 2024 (npj Viruses) - R code for influenza A transmission thresholds in ferrets.
Zoonoticpyrenew-flu-light
A replication in Python and PyRenew of a renewal model written in Epidemia for forecasting influenza hospital admissions.
Epidemiologyseqsender
Automated pipeline to generate FTP files and manage submission of sequence data to public repositories including NCBI GenBank.
Softwarezoe
Zoe provides both broad and highly specialized implementations for bioinformatics, focusing on common data formats and methods.
Software