Whole genome sequencing and assembly

Why are we doing this?

You are not doing whole genome sequencing, but it is an important part of modern genetics, so we should learn how it is done.

Most sequencing projects require assembly, including yours, so it is important to learn about.

Assembly: When DNA is sequenced with multiple reads, or DNA is sequenced in multiple fragments, and the sequences get pieced together to determine the sequence of the original DNA

Learning Goals

By the end of this unit, you should be able to describe

• the process of whole genome shotgun sequencing.

• the process of sequence assembly

• why it is necessary to fragment the genome prior to sequencing

• why repeats make whole genome assembly difficult

You will simulate the assembly of whole genome sequence data using part of the Jaberwocky poem by Lewis Carroll

Reading: Whole genome sequencing

Read this for a description of whole genome shotgun sequencing and terms defined, and a description of the Jabberwocky activity

Activity: Assemble a genome

Watch the above videos, read Handout: Whole genome sequencing described.

This is a simulated genome (it's actually part of the Jabberwocky poem by Lewis Carroll). The genome has been fragmented, and the fragments were sequenced. Your job is to assemble the sequences to determine the original genome sequence.

Click here to access the simulated DNA sequences. Click "Make a copy" to make a copy in your Google drive that you can edit.

Move the sequence reads around (pieces of text) to assemble the genome. Remember you can only join two sequence reads if they have overlapping DNA sequences.

Submit your assembly under Assignment: Assembly 1

Assignment: Assembly 1

Assemble the "genome" above and answer these questions

Activity: Assemble a genome containing repeats

Watch the above videos, read Handout: Whole genome sequencing described.

This is a simulated genome containing repeats (It's also part of the Jabberwocky poem, and I added repeats). The genome was fragmented, and the fragments were sequenced, just like in whole genome sequencing. Your job is to assemble the sequences to determine the original sequence.

Click here to access the simulated DNA sequences to assemble them. Click "Make a copy" to make a copy in your Google drive that you can edit.

Submit your assembly under Assignment: Assembly 2

Assignment: Assembly2

Assemble the "genome" containing repeats above, and answer these questions