All Resources
Browse the complete collection of CDC Influenza Division resources, or use the navigation to filter by category.
Automated 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.
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...
TrainingMIRA
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.
LaboratoryMRT-PCR of Influenza A Viruses for Sequencing (Rev01D)
Multi-segment reverse transcription PCR protocol for amplifying influenza A virus genome segments for sequencing. Superseded by Rev02D.
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.
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.
LaboratoryNative Library Prep & Nanopore Sequencing of InfA Virus & SARS-CoV-2 S-gene Amplicons (Rev00D)
Protocol for native library preparation and Oxford Nanopore sequencing of influenza A virus and SARS-CoV-2 S-gene amplicons. Superseded by Rev01D.
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.
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.
Laboratoryam4N1Phylogenetics
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.
SoftwareeditMSA
A collection of scripts for editing and manipulating multiple sequence alignment files.
Softwareflu-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.
ZoonoticoctoFLU
Script that labels phylogenetic clades based on the clade of the nearest neighbor using patristic distances determined from the tree.
Softwarepyrenew-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