Resources & Reports

Resources & Tools

Primer design for amplicon-based sequencing

Primal Scheme

Primer sets for amplicon sequencing of multiple pathogens.

Genome assembly and quality control

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.

Outbreak transmission and analysis

Delphy

Rapid phylogenetic tree construction for large datasets.

ReconstructR

R package for transmission reconstruction.

Laboratory Protocols

Viral-Amplicon-Pipeline

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

Reports

Reports generated by the NE PGCoE will be made available here when ready.