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# cov2Vero ref genome with STAR index

Combines, in this order
 * SARS-CoV-2 strain WuHan-1 [NC_045512.2](https://www.ncbi.nlm.nih.gov/nuccore/NC_045512.2)
 * Hg38 ([Human GRCh38/seqs_for_alignemtn_piplines.ucsc_ids](ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/001/405/GCA_000001405.15_GRCh38/seqs_for_alignment_pipelines.ucsc_ids/))

and then indexes the combined genome with STAR (overhang=100), BWA, 

For use with the [CCTS-Informatics-Pipelines](CCTS-Informatics-Pipelines)/[Snakemake-Eukaryotic-RNAseq-Pipeline](CCTS-Informatics-Pipelines/Snakemake-Eukaryotic-RNAseq-Pipeline)

Edit config.yaml of the Snakemake-Eukaryotic-RNAseq-Pipeline to set 
```
  # required for RNA-Seq analysis
  index:      "/data/project/public_datasets/ngs/genomes/cov2WuHan1_hg38/cov2WuHan1_hg38noAlt/STAR/STAR_2.5.3a-100"
  annotation: "/data/project/public_datasets/ngs/genomes/cov2WuHan1_hg38/cov2WuHan1_hg38noAlt/cov2WuHan1_hg38noAlt.gtf"
  # optional - for bwa alignment
  bwa:        "/data/project/public_datasets/ngs/genomes/cov2WuHan1_hg38/BWA/0.7.13/cov2WuHan1_hg38noAlt.fa"
  # optional - for creating sample-specific genomes
  cov2:       "/data/project/public_datasets/ngs/genomes/cov2WuHan1_hg38/cov2WuHan1/NC_045512.2.fasta"
```