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

MIRA: Portable, Interactive Application for High-Quality Influenza, SARS-CoV-2 and RSV Genome Assembly, Annotation, and Curation

IRMA (the Iterative Refinement Meta-Assembler) is a highly configurable and adaptive tool for virus genome assembly.

Zoe provides both broad and highly specialized implementations for bioinformatics. In particular, we focus on common data formats and methods relevant for the sequencing of RNA viruses.

A tool to aid virus sequencing and accelerate IRMA.

Lineage and clade classifier for influenza sequences

Bioinformatics related user-defined functions for Cloudera Impala.

A collection of scripts for editing and manipulating multiple sequence alignment files.

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

Protein analysis pipeline for characterizing influenza antigenic drift

For producing amino acid difference tables for other applications.

A collection of low-dependency, bioinformatic format and data conversion scripts.