4  Download Workshop Data

Download the workshop data

1. Create a new folder on your computer desktop called BM425_Workshop
2. Download the files from the sections below into this new folder.

4.1 Sequencing reads for SARS-CoV-2 assembly

• Illumina paired-end reads, forward direction (trimmed_pe_aln.qsorted.mapped.fixed.1.fastq.gz)
• Illumina paired-end reads, reverse direction(trimmed_pe_aln.qsorted.mapped.fixed.2.fastq.gz)

4.2 SARS 2003 genome for genome comparison

• SARS 2003 genome sequence (.fasta)(SARS_AY278741.fasta)
• SARS 2003 annotation (.gff3)(SARS_AY278741.gff3)
• SARS 2003 combined genome sequence and annotation (.gbk)(SARS_AY278741.gbk)

4.3 Dutch SARS-CoV-2 reads for genome comparison

• GridION reads for March 2020 Dutch isolate(ERR4164769_1.fastq.gz)

Your Working Directory

When you have downloaded all the files required for the workshop, the contents of the BM425_Workshop folder should resemble the image in Figure 4.1.

Figure 4.1: macOS BM425_Workshop folder with all files downloaded.