Project

From Woof to SNP

7 completions
~ 12 hours
4.3

In this project, you will create a pipeline for the identification of SNPs using NGS data. You will learn how to work with the NCBI Sequence Read Archive database, perform quality control of sequence data in FASTQ format, build alignments to reference genomes, and find SNPs with the IGV genome browser.

Provided by

Edvancium Edvancium

About

Like humans, dogs can be predisposed to various diseases, for example, Degenerative Myelopathy. One of your friends recently learned about this disease and wants to know if their Welsh Corgi dog is at risk. You are tasked with helping to investigate whether there is a variation in the dog's genome associated with this predisposition. The replacement of just one nucleotide in the DNA chain is called single-nucleotide polymorphism (SNP). Such variations affect disease development, pathogen response, and visual and physiological features, moreover, they are the markers of other genetic mutations. In this project, you will create a pipeline for the identification of SNPs, associated with such a fatal disorder for Welsh Corgi.

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Training project

This project allows you to practice and strengthen your coding skills, helping you get ready for more advanced tasks ahead.

What you'll learn

Once you choose a project, we'll provide you with a study plan that includes all the necessary topics from your course to get it built. Here’s what awaits you:
You have preprocessed reads, so as you should always check the quality and remove adapters from your data.
Find, explore, and download the Canis lupus familiaris reference genome from NCBI and GenBank databases. Moreover, the genome should be indexed for future alignment.
Align the provided data to the reference genome with the bowtie2 tool. Then compare reference and experimental sequences with the IGV browser, find the coordinates, and view the SNP in the provided sample.
Add annotation and find the gene of SNP location.
Read an article about the SNP to learn more about the disease.
Read an article about the SNP to learn more about the disease.
Read an article about the SNP to learn more about the disease.

Reviews

Ethan Aidam avatar
Ethan Aidam
1 year ago
Great way to begin learning how to create a bionformatics pipeline to search for mutations in a sequenced genome with Bash scripting.

4.3

Learners who completed this project within the course rated it as follows:
Usefulness
5.0
Fun
4.0
Clarity
4.0