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CSE 5370: Bioinformatics Homework 2: Due Thursday, February 24th, 2022 at 4:59PM CST

This homework assignment involves writing code to generate synthetic genomic data and use it to test two genome assembly algorithms: greedy shortest common superstring (SCS) and de Bruijn graphs. Students will generate three pools of synthetic reads from a random genome and use each pool to run the assembly algorithms with varying parameters. Code and results must be submitted. Group work is allowed but each student must generate their own unique read pools and submissions.

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55 views3 pages

CSE 5370: Bioinformatics Homework 2: Due Thursday, February 24th, 2022 at 4:59PM CST

This homework assignment involves writing code to generate synthetic genomic data and use it to test two genome assembly algorithms: greedy shortest common superstring (SCS) and de Bruijn graphs. Students will generate three pools of synthetic reads from a random genome and use each pool to run the assembly algorithms with varying parameters. Code and results must be submitted. Group work is allowed but each student must generate their own unique read pools and submissions.

Uploaded by

Dhruv Surani
Copyright
© © All Rights Reserved
We take content rights seriously. If you suspect this is your content, claim it here.
Available Formats
Download as PDF, TXT or read online on Scribd
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CSE 5370: Bioinformatics

Homework 2

Due Thursday, February 24th, 2022 at 4:59PM CST

In this homework you will write basic genome assemblers using two methods:
greedy SCS and De Bruijn Graphs.

StackOverflow.com & Similar Sites


Use of stackoverflow.com and other sites is explicitly allowed (industry re-
serachers and academic labs use these sites frequently). However, for this
course you must include a comment in your code with the link to the page
you referenced whenever these sites influence your own code writing. For ex-
ample, when writing this homework assignment I forgot how to insert code into
LATEXdocuments and recalled how to after visiting stackoverflow.com. If I were
submitting this as an assignment, I would want to include a comment like the
below example in my code submission:

1 %When writing this homework assignment, I did not recall how to


2 %insert code in a nice looking way into LaTeX documents,
3 %so I referred to this page on stackoverflow for help:
4 %https://stackoverflow.com/questions/3175105
5 \usepackage{minted}
6 \begin{minted}[mathescape, linenos]{python}
7 Code To Insert in \LaTeX...

Group Work
You are allowed to work together in groups of up to 4, but the assignment is
structured so that every person must generate their own synthetic read pools
with a random number generator (such that every submission will be unique).
You may collaborate on discussing logic in the code. The automated grading
script automatically renames all functions: function1, function2, function3 etc.
and all variables: var1, var2, var3 etc. then standardizes all white space. Code
from different groups should not be identical after this process and every person
should have a different random set of reads and assemblies per the assignment
specification.

1
1 Simulated Reads (25 points)
1. Write python code to generate a synthetic genome (a string) consisting of
random nucleotide sequence of length 10,000.
2. Randomly generate a pool of synthetic ”reads” (Pool A) of length 250
such that no reads overlap on the genome from 1.
3. Randomly generate a pool of synthetic ”reads” (Pool B) such that every
nucleotide in the genome from 1 is in a minimum of 4 reads and each read
is guaranteed to overlap with another read by at least 7 nucleotides.
4. Randomly generate a pool of synthetic ”reads” (Pool C) such that every
nucleotide in the genome from 1 is in a minimum of 30 reads and each
read is guaranteed to overlap with another read by at least 14 nucleotides.

Use a random number generate to produce these read pools and submit them
as text files with the assignment. Also include in your submission a text files
containing your synthetic genome. Include the code to generate these in your
single code file.

2 Greedy SCS (35 points)


Modify the below code such that it is greedy and run on your 3 files with
min length=9. Include three separate text files containing the output for run-
ning your greedy SCS implementation on each of the three read pools from
section 1. Also include your code.
1 import itertools
2

3 def overlap(read_a, read_b, min_length=1):


4 start = 0 # start all the way at the left
5 while True:
6 start = read_a.find(read_b[:min_length], start)
7 if start == -1:
8 return 0
9 if read_b.startswith(a[start:]):
10 return len(read_a)-start
11 start += 1
12

13 def shortestCommonSuperstring(string_set):
14 shortest_sup = None
15 for perm in itertools.permutations(string_set):
16 sup = perm[0]
17 for i in range(len(string_set)-1):
18 olen = overlap(perm[i], perm[i+1], min_length=1)
19 sup += perm[i+1][olen:]

2
20 if shortest_sup is None or len(sup) < len(shortest_sup):
21 shortest_sup = sup
22 return shortest_sup

3 De Bruijn Graphs (40 points)


Write a de bruijn graph and run it on each of your three read pools from section
1 three times (9 total output files) with

k = 1, 9, 18

for each run. Include a text file with the assembly output in your submission as
well as your code.

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