https://github.com/cdcgov/seqsender

Automated Pipeline to Generate FTP Files and Manage Submission of Sequence Data to Public Repositories

bioinformatics-pipeline biosample cdc cdc-influenza-division genbank gisaid gisaid-format gisaid-upload gisaid-uploader ncbi-biosamples ncbi-genbank ncbi-sra ncbi-submission ncird ncird-id seqsender sra

Last synced: 20 Feb 2026

https://github.com/cdcgov/novel-flu-detection

cdc-influenza-division ncird ncird-id

Last synced: 13 Apr 2025

https://github.com/cdcgov/flu-nursing-home-model

cdc-influenza-division ncird ncird-id

Last synced: 13 Apr 2025

https://github.com/cdcgov/clean-genes

A rust crate that automatically cleans up a gene alignment by trimming to ORF and identifying and/or removing problematic sequences.

bioinformatics cdc-influenza-division data-cleaning data-normalisation data-normalization data-science fasta ncird ncird-id sequence-alignment sequence-analysis sequence-annotation

Last synced: 01 Mar 2026

https://github.com/cdcgov/sswsort

A simple tool for classifying gene segments

bioinformatics cdc-influenza-division ncird ncird-id

Last synced: 13 Apr 2026

https://github.com/cdcgov/classifying-influenza-trends

Code repository for published manuscript

cdc-influenza-division hospitalization-data influenza ncird ncird-id r

Last synced: 04 Apr 2026