PLNT4610/PLNT7690 BIOINFORMATICS

Assignment 4

Genome Assembly


 This assignment is worth 20% of the course grade.

Due: December 5, 2024


Goal: To test how low coverage of a genome affects the quality of a genome assembly. 

Rationale

The purpose of this assignment is to learn the steps of assembling a small eukaryotic genome, and some of the conditions affecting the quality of the assembly. Because of limited disk space for student accounts, we don't have the luxury of using the complete set of sequencing reads. Therefore, this assignment will create files containing a subset of data from the published read set, and attempt to assemble the genome using this smaller dataset.

The procedures for assembling a genome are described in the Genome Assembly tutorial. In the original tutorial, a dataset using 5% of the published reads was used to demonstrate the process. In this assignment, you will create a larger dataset, representing 10% of the total reads, to see if better coverage of the genome will result in a better assembly.

Main steps:
1. Create a sample set of sequencing reads.
2. Assemble R. diobovatum genome as described in the Genome Assembly tutorial, replacing the data used in the tutorial with your own dataset.
3. Discuss your results, in comparison to the data from the original tutorial.

This assignment will be done using the Biolegato application blreads. You can get an idea of how blreads works in the YouTube video BIRCH - Desktop Bioinformatics (long version). The section on blreads begins at 8:53 in the video.

0.  Complete the Genome Assembly tutorial

Make sure to read the introductory page at the beginning of the tutorial. In particular, note that as the assembly progresses, the results of each step appear in a new directory, with naming to indicate the steps that produced the files in that directory.

Because the assembly process is fairly complex, first run through the tutorial using the data from the tutorial. Student accounts are limited to 1 Gb of disk space. However, students may claim an extra 5 Gb of space as described in the tutorial on Obtaining Extra Disk Space. Do the tutorial in /local/workspace01/tutorials.

After completing the Genome Assembly tutorial, you should be ready for the next steps.

1. (3 points) Create a sample dataset of sequencing reads.


Note: To avoid running out of disk space in your /local/workspace01 directory, it is okay to delete the genome_assembly directory from the Genome Assembly Tutorial. You will need about 3 Gb to complete
this assignment. Check your disk quota in the directory you plan to work in using 'quota -v'.

Assuming that you previously obtained your extra diskspace, create a directory for Assignment 4 as follows:

Go to your as4 directory, and then type

mkdir /local/workspace01/userid/assembly
chmod a+x /local/workspace01/userid
ln -s /local/workspace01/userid/assembly
chmod a+rx /local/workspace01/userid/assembly

You will now have in your as4 directory a symbolic link called assembly. For this assignment, the report should be in the as4 directory, but all steps in the genome assembly process will be done in the assembly directory.

Next, in your assembly directory, create a directory called reads. Launch blreads in the reads directory. blreads shows the contents of the current directory, which in this case is empty.



Choose File --> Create symbolic links to files in another directory. Set the Source Directory to /home/psgendb/courses/PLNT4610/as4. Set pattern to match to "*.gz". This will create symbolic links to all gzipped read files in the PLNT4610 as4 directory.

The links will appear in the blreads window. Note that symbolic links are indicated by the letter "l" in the Type column.

You can also verify that the creation of the links at the command line:

lrwxrwxrwx 1 frist drr 64 Nov  6 20:21 DL300_S1_L001_R1_001.fastq.gz -> /home/psgendb/courses/PLNT4610/as4/DL300_S1_L001_R1_001.fastq.gz
lrwxrwxrwx 1 frist drr 64 Nov  6 20:21 DL300_S1_L001_R2_001.fastq.gz -> /home/psgendb/courses/PLNT4610/as4/DL300_S1_L001_R2_001.fastq.gz
lrwxrwxrwx 1 frist drr 64 Nov  6 20:21 DL400_S2_L001_R1_001.fastq.gz -> /home/psgendb/courses/PLNT4610/as4/DL400_S2_L001_R1_001.fastq.gz
lrwxrwxrwx 1 frist drr 64 Nov  6 20:21 DL400_S2_L001_R2_001.fastq.gz -> /home/psgendb/courses/PLNT4610/as4/DL400_S2_L001_R2_001.fastq.gz
lrwxrwxrwx 1 frist drr 64 Nov  6 20:21 DL700_S3_L001_R1_001.fastq.gz -> /home/psgendb/courses/PLNT4610/as4/DL700_S3_L001_R1_001.fastq.gz
lrwxrwxrwx 1 frist drr 64 Nov  6 20:21 DL700_S3_L001_R2_001.fastq.gz -> /home/psgendb/courses/PLNT4610/as4/DL700_S3_L001_R2_001.fastq.gz

In some bash configurations, live symbolic links will appear in a aqua color, and gzipped files are highlighted in red.

You will create your dataset using SeqKit to generate a random sample of 10% of the reads in the original files. Before running SeqKit sample you have to run guesspairs.py, which groups together read files into left and right reads. SeqKit has to know which files go together, because it has to make sure that if a left read is sampled, then the right read also appears in the sample.
 

As described previously in the Genome Assembly tutorial, start by selecting the original read files (.fastq.gz), and then File --> guesspairs.py. By default "R1" and "R2" will be used to identify the left and right read files for each set of paired-end reads. Click on Run, and a new blreads window will pop up with the files organized in pairs.




In blreads, select all the read files and choose Reads --> SeqKit sample. Set "prefix to prepend" to "_S10, and set Percentage of sequences" to 10.
Click on Run.


The sample files have the same name as the original files, with the addition of "_S10" to the names.

Note that while the symbolic links have a very small size, the sizes of the sample files indicate that these are read files, not links.

The sample files will be your dataset for all subsequent steps.

As a check that the sample files were created correctly, we expect that the sample files should be about 1/10 the size of the original files. In blreads, the size of the sample files is shown, but the sizes of the original files are not, because blreads is showing the symbolic links to those files, rather than the files themselves. Fortunately, the ls command has the -L option that shows the size of the file the link points to, rather than the link itself. In the reads directory type

ls -lL

to see both the original and sample files for comparison. 

2. (10 points) Assemble the genome using your dataset.

In this section you will follow the Genome Assembly tutorial to assemble the R. diobovatum genome from your sample dataset.

a) Create symbolic links with short names to your sample read files

 Your genome assembly begins at step 0, but there are some differences. Note that the read files in step 0 have names containing the word "sample" eg. DL300_S1_L001_R2_001_sample.fastq.gz, whereas your read files will contain the string "_10" eg. DL300_S1_L001_R1_001_S10.fastq.gz. In step 0, you will create symbolic links with short names for use in the remainder of the tutorial. To minimize confusion, it is probably best to just use the same short names as seen in the tutorial. For example, after creating the link and renaming it, the link to DL300_S1_L001_R1_001_S10.fastq.gz would have the name DL300_R1.fastq.gz. From this point, filenames should appear exactly as shown in the tutorial.

IMPORTANT!: This is a tedious but very important step. When creating links, you need to make absolutely sure that you are choosing the correct target file (which includes "S10"), and making sure that the string you plan to change is found in the target filename. To verify that you have all six symbolic links done correctly, type ls -l *R[12].fastq.gz, which should give the following output:

lrwxrwxrwx 1 frist drr 33 Nov  7 15:08 DL300_R1.fastq.gz -> DL300_S1_L001_R1_001_S10.fastq.gz
lrwxrwxrwx 1 frist drr 33 Nov  7 15:09 DL300_R2.fastq.gz -> DL300_S1_L001_R2_001_S10.fastq.gz
lrwxrwxrwx 1 frist drr 33 Nov  7 15:10 DL400_R1.fastq.gz -> DL400_S2_L001_R1_001_S10.fastq.gz
lrwxrwxrwx 1 frist drr 33 Nov  7 15:15 DL400_R2.fastq.gz -> DL400_S2_L001_R2_001_S10.fastq.gz
lrwxrwxrwx 1 frist drr 33 Nov  7 15:11 DL700_R1.fastq.gz -> DL700_S3_L001_R1_001_S10.fastq.gz
lrwxrwxrwx 1 frist drr 33 Nov  7 15:12 DL700_R2.fastq.gz -> DL700_S3_L001_R2_001_S10.fastq.gz

Do not proceed until you get this right! Note that the blreads File menu also has a delete function, if you want to delete specific links that were made incorrectly. You can also use the Edit --> blsort, to your advantage to make it easier to look at groups of file names.

b) Calculate the genome coverage of your experimental dataset

In this step, you will calculate the ideal read coverage for sequencing the R. diobovatum genome, as well as the actual coverage of the full dataset, and the sample datasets.

Save the LibreOffice spreadsheet file coverage_template.ods to your as4 directory as coverage.ods. In coverage.ods, fill in the formulae  needed to calculate the number of reads for 1-fold coverage, as well as 50-fold coverage, for a genome of 21,000,000 bp using 150 nt reads. The coverage statistics for the full dataset and the sample dataset from the tutorial are also  included in this file. Note that the "actual coverage" calculations depend on the 1-fold coverage calculation in cell B9.

Once you have completed those calculations, run Reads --> SeqKit stats to generate statistics for your own sample reads. To save the SeqKit results, choose Edit --> Select All and then File --> Save SELECTION As. Set File format to tsv, and type in the filename S10stats.tsv. Open your S10stats.tsv file in LibreOffice Calc, and paste the statistics into the rows provided in coverage.ods.

In your report, you will be asked to summarize the findings from this section.

c) Assemble your reads using Abyss, Spades and SOAPdenovo2.

Save a copy of assemblies_template.ods to your as4 directory under the name assemblies_S10.ods.

Follow the steps in the Genome Assembly tutorial to create genome assemblies using Abyss, Spades and SOAPdenovo2. As you complete each assembly, copy the results for scaffolds to your assemblies_S10.ods file. The spreadsheet for these results should pop up in LibreOffice each time a Quast run is complete. Alternatively, this data can be found in the quast_results/transposed_report.tsv for each assembly.


Additional notes:

3. (5 points) Conclusions - What have you learned?

4. (2 points) Presentation.

Part of the grade will be determined by the quality of your web page(s) for the assignment, including:

How to get started

1. Create a directory called either public_html/PLNT4610/as4 or public_html/PLNT7690/as4. Make this directory world-readable and world executable.

2. Do  all work in the as4 directory. That way, all your files will already be where they need to be.

What you need to complete your assignment

Your report should include the following:

1. Output from   ls -l *R[12].fastq.gz, showing the short name symbolic links to your experimental read files.

2. Briefly summarize the coverage results, and provide links to the following files:
3. Conclusion - Brief discussion of results, as described above.
How to post it

1. Create a new HTML file called as4/as4.html. Your web page for Assignment 4 should take the form of a report, that makes it easy to figure out what you did.

2. Make all files in the as4 directory world-readable (chmod a+r *).

3. cd into your assembly directory and type

correct

The correct script descends recursively through a directory tree, making all files world-readable and all directories world readable and searchable.

3. Edit either PLNT4610.html or PLNT7690.html to include a link to as4/as4.html.

4. In the Firefox or SeqMonkey Browser, go to your home page and follow all hypertext links to your assignment, and test all links to your output files.

5. If you paste excerpts of output into a web page, change the output section to a fixed font such as Courier, or set the style to "Preformat". The output from most sequence programs assumes that each character takes up an equal amount of width, which is not true for proportional fonts such as Helvetica or Times.

Academic integrity: Your work is assumed to be your own original work. All University policies regarding academic integrity apply.

On the day the assignments are due, I should be able to just go to each person's web site and find the output. You don't need to send me an email message saying that your assignment is complete. If you choose not to hand in this assignment, you don't need to do anything.

Approximate running times

The actual execution times required for each step will vary depending on the load on the system, but here are some typical "wall clock" times for jobs requiring more than 1 min. for this dataset:

program
 time (min.)
Trimmomatic
 2
pollux
 8
abyss
 9
spades
 6
SOAPdenovo2
 7

For this dataset, you can assume that all other programs run in a short time.