COVID

SARS-CoV-2 analysis with Cecret

The default settings for Cecret are for SARS-CoV-2 sequencing, specifically the 2019 or 2020 outbreak.

graph LR
     subgraph core workflow
     A[fastq files]-->B[seqyclean or fastp]
     B --> C[bwa or minimap2]
     C --> D[ivar trim or samtools ampliconclip]
     D --> E[ivar consensus]
     end
     subgraph SARS-CoV-2 specific
     E --> F[pangolin]
     E --> G[vadr]
     E --> H[nextclade]
     D --> I[freyja]
     end

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The parameters for core portion of the workflow are covered on a different wiki page, but there are some relevant parameters that will also discussed here.

1. The reference genome
2. bed files
3. gff file

The parameters used for SARS-CoV-2 sequencing with their default values: