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CLC Genomics Workbench

Objective

To demo CLC Genomics Workbench, proprietary bioinformatic software, useful for visualization and data processing.

Exercises

Working with real data.

  1. Download the three files: human_g1k_v37.fasta, reads.tumour.fastq, reads.normal.fastq Note: If you don’t want to split the fastq files yourself, only download the Human glk v37 fasta and then download the split_r1_r2.zip file below.
  2. Either follow along with Loading data to split the fastq files from compiled read 1 and 2 to separate files or download the split_r1_r2.zip with the files already split.
  3. Zoom recordings from 2020 are available for stream or by download from gdrive (transcript) for the resequencing analysis using tracks tutorial. A second zoom video recording is available with this link (or by download, transcript) which finishes the resequencing tutorial and continues into the de-novo genome assembly tutorial.
  4. To download the genome sequences for the Denovo assembly tutorial use the following links SRR396639_1.fastq.gz, SRR396639_2.fastq.gz, SRR396640_1.fastq.gz, and SRR396640_2.fastq.gz. Please note that SRR396639_1/2 is a mate-pair library while SRR396640_1/2 are standard paired-end sequences.