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