Introduction to the Course Dataset
The dataset for this course is a benchmark dataset for the WGS analysis of SARS-CoV-2. The Variants of Interest/Variants of Concern (VOI/VOC) lineages study validated a lineage-calling pipeline with 16 samples from CDC-defined lineages. The dataset has been described in detail here: https://github.com/CDCgov/datasets-sars-cov-2
In week 1, we will analyse one sample from the VOI/VOC dataset. You can download the sequence data for this sample using the following command (the sample identifier below is the accession number for the data in the European Nucleotide Archive (ENA)):
fastq-dump --split-files ERR5743893
The Wuhan-1 reference sequence, which we’ll use when we map the sequence data for ERR5743893, is attached in a file named, “MN908947.fa”
Bioinformatics for Biologists: Analysing and Interpreting Genomics Datasets
Bioinformatics for Biologists: Analysing and Interpreting Genomics Datasets
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