This repository is a collection of workflows hosted by the StaPH-B community to provide a centralized location for SARS-CoV-2 workflow development.
-
Titan Illumina PE: Workflow for processing raw Illumina Fastq Paired End reads and generating consensus genome assemblies with a variety of QC metrics.
-
Titan Illumina SE: Workflow for processing raw Illumina Fastq Single End reads and generating consensus genome assemblies with a variety of QC metrics.
-
Titan ONT: Workflow for processing raw ONT reads (Fastq or Fast5 format) and generating consensus genome assemblies with a variety of QC metrics.
-
Titan Clear Labs: Workflow for processing reads obtained from the Clear Labs sequencing approach and generating consensus genome assemblies with a variety of QC metrics.
-
Mercury: Workflow for uploading genomic sequence data into GISAID, NCBI-GenBank, and NCBI-SRA
- Workflows originally derived from Theiagen's:
- Public Health Viral Genomics repository.
- Design influenced by UPHL's Cecret
- Design influenced by StaPH-B's Monroe