Sars-Cov-2
The Sars-Cov-2 workflow is an amplicon sequencing pipeline used to detect variants in Covid test samples. It simply takes in raw NGS reads.
Quick Start
- Find Sars-Cov-2 in “Explore” and click “add” to add it to your workflows
- Open Sars-Cov-2 in “Workflows” by clicking “View”
- Enter parameters for Sars-Cov-2
- Launch workflow
- Results appear in Latch Data within 3-5 minutes
How the pipeline works
- Use fastv to count kmers with respect to SARS Cov-2 or human genomes as a means to pre-screen false positives.
- Construct a genome assembly using bowtie2 using the wuhan genome as a reference.
- Construct a consensus sequence from the assembly using ivar.
- Clade analysis of consensus using nextclade.
- Lineage analysis of consensus using pangolin.
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