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 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 bowtie2 using the wuhan genome as a reference.
  3. Construct a consensus sequence from the assembly using ivar.
  4. Clade analysis of consensus using nextclade.
  5. Lineage analysis of consensus using pangolin.