> ## Documentation Index
> Fetch the complete documentation index at: https://wiki.latch.bio/llms.txt
> Use this file to discover all available pages before exploring further.

# 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

1. Find Sars-Cov-2 in "Explore" and click "add" to add it to your workflows
2. Open Sars-Cov-2 in "Workflows" by clicking "View"
3. Enter parameters for Sars-Cov-2
4. Launch workflow
5. Results appear in Latch Data within 3-5 minutes

### How the pipeline works

1. Use [fastv](https://github.com/OpenGene/fastv) to count kmers with respect to SARS Cov-2 or human genomes as a means to pre-screen false positives.
2. Construct a genome assembly using b[owtie2](http://bowtie-bio.sourceforge.net/bowtie2/index.shtml) using the wuhan genome as a reference.
3. Construct a consensus sequence from the assembly using [ivar](https://github.com/andersen-lab/ivar).
4. Clade analysis of consensus using [nextclade](https://clades.nextstrain.org/).
5. Lineage analysis of consensus using [pangolin](https://github.com/cov-lineages/pangolin).