Homework Week 11

1. Explain basic principles of Nanopore sequencing. (10pts total)

Find peer-reviewed information about the Nanopore sequencing technique as employed by Oxford Nanopore Technologies (ideally including at least one describing the MinION technology in detail). Cite the references you found useful to address the following questions (0.5 pts for the citations alone)

• In one sentence, summarize the principle of Nanopore sequencing. (1pt)
• Label the following image. (2.5pts)
• Describe 2 properties that the molecule labeled with (4) must have. (2pts)
• Where is the change of current registered? (1pt)
• Which naturally occuring types of proteins could be used for the molecule labeled with (2) and why, i.e. what are the properties that are needed? (1pt)
• There are three types of adapters that are ligated to the DNA prior to sequencing. Explain their functions. (3pts)

2. Describe 2 advantages and 2 disadvantages of Nanopore sequencing compared to Illumina-based sequencing. (4pts total)

3. Basic QC (3pts total)

• Run FastQC on the Nanopore fastq files in this folder: /home/frd2007/ANGSD_2019/nanopore_seq/guppy_out/. (1pt)
• Describe 2 observations that seem very different when compared to FastQC results of Illumina-based runs. (2pts)