Primal Scheme

Primer sets for amplicon sequencing of multiple pathogens.

viral-ngs

Assembly and analysis of viral NGS data.

TheiaCoV Workflow Series - Public Health Bioinformatics

Workflow series for genomic characterization of SARS-CoV-2.

TheiaProk Workflow Series - Public Health Bioinformatics

Workflow series for genomic characterization of bacteria.

TheiaMeta - Public Health Bioinformatics

Assembly and analysis of metagenomic sequencing data.

virus-shotgun

Viral characterization and SNP identification.

bacpage

Bacterial assembly and analysis, currently optimized for V. cholerae.

JUNIPER

A framework for predicting both phylogenies and transmission networks for viral outbreaks, accounting for both within-host variability and incomplete data.

Delphy

A fast, scalable, accurate, and accessible tool for Bayesian phylogenetics with a drag-and-drop interface that requires no local installation or coding.

ReconstructR

An R package that allows for prediction of transmission events in infectious disease outbreaks and can account for within-host variability.

Phylosamp Work Instruction

The MA DPH developed a work instruction covering the uses of the phylosamp R package for the purpose of sample sizing for viral variant surveillance. Example code, outputs, and detailed instructions are provided to perform power analyses and sample sizing for surveilling viral variants.

Viral-Amplicon-Pipeline

Automated viral amplicon sequencing methods and scripts for Hamilton liquid handlers.

Broad Institute Metagenomic Sequencing Protocol

Pooled metagenomics sequencing protocol (paired with hybrid capture using the Twist Comprehensive Viral Research Panel) that greatly decreases library preparation costs by allowing 24–96 samples to be processed through a single shared downstream reaction after reverse transcription.