Software
Software tools, bioinformatics pipelines, and related technical resources from the CDC Influenza Division.
Genome Assembly
IRMA
IRMA (the Iterative Refinement Meta-Assembler) is a highly configurable and adaptive tool for virus genome assembly.
MIRA
MIRA: Portable, Interactive Application for High-Quality Influenza, SARS-CoV-2 and RSV Genome Assembly, Annotation, and Curation.
MIRA-NF
Nextflow implementation of MIRA for scalable, high-quality influenza, SARS-CoV-2 and RSV genome assembly, annotation, and curation.
irma-core
A tool to aid virus sequencing and accelerate IRMA.
Classification & Annotation
KARMAflu
K-mer Assisted Reassortant Mapping Algorithm for Influenza.
label
Lineage and clade classifier for influenza sequences.
octoFLU
Script that labels phylogenetic clades based on the clade of the nearest neighbor using patristic distances determined from the tree.
sswsort
A simple tool for classifying gene segments.
Pipelines & Data
NCBIH5N1MetadataParser
Scripts and environment to perform ETL on NCBI data for H5N1.
app-squared
Protein analysis pipeline for characterizing influenza antigenic drift.
seqsender
Automated pipeline to generate FTP files and manage submission of sequence data to public repositories including NCBI GenBank.
Sequence Utilities
aadiff
For producing amino acid difference tables for other applications.
clean-genes
A rust crate that automatically cleans up a gene alignment by trimming to ORF and identifying and/or removing problematic sequences.
editMSA
A collection of scripts for editing and manipulating multiple sequence alignment files.
ifx-convert
A collection of low-dependency, bioinformatic format and data conversion scripts.
Libraries
hubhelpr
R package providing helper functions for CDC forecast hub maintenance and report generation.
udf-bioutils
Bioinformatics related user-defined functions for Cloudera Impala.
zoe
Zoe provides both broad and highly specialized implementations for bioinformatics, focusing on common data formats and methods.