CLC Genomics Workbench¶
Objective¶
To demo CLC Genomics Workbench, proprietary bioinformatic software, useful for visualization and data processing.
Exercises¶
Working with real data.
- 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.
- 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.
- 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.
- 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.
Resources¶
System Requirements for CLC Genomics Workbench
Resequencing Analysis using Tracks tutorial
Denovo assembly and blast notes
DeNovo paired-end assembly notes
Class Recordings¶
- Session 33 recorded April 12th 2021. A trancscript of the recording is also availabile.
- Session 34: recorded April 14th 2021. A trancscript of the recording is also availabile.
- Session 35: recorded April 16th 2021. A trancscript of the recording is also availabile.
- Session 36: recorded April 19th 2021. A trancscript of the recording is also availabile.
- Session 37: recorded April 21st 2021. A trancscript of the recording is also availabile.
- Session 38: recorded April 23rd 2021. A trancscript of the recording is also availabile.
Last modified 23 April 2021. Edits by Ross Whetten, Will Kohlway, & Maria Adonay.