Type of analyses Which can be performed on Whole Genome Data

Question

[Umer]

Hey everyone, This might be a nieve question, kindly spare me. I want to know about type of analyses which can be performed on whole genome sequence data. For example, say I have whole genome data of like 4 different cattle breeds of xyz country. The one analysis i know that can be performed is Variant (SNP,Indel) analysis. I want to know what else i can do with that sequence data. Any analysis name or pipeline which can be used for further insights into the data ? Help will be greatful. Thank you.

[4galaxy77]

What's your aim for the project? What questions are you trying to answer or what aspects of biology are you interested in?

[Umer]

Hey, My main objective is to learn different bioinformatics pipelines and protocols to study WGS data. Long with that I've to complete my Thesis with something new. The sample data I've got is already published with a Variant study. So i wanted to find something new which could be performed and learnt.

Answer 1

[Chris Dean]

I would first recommend browsing the ruminant literature to see what has/can be done with this type of data, but here are a couple of suggestions to get you started.

You mentioned the possibility of identifying single nucleotide polymorphisms and indels. This could be used to identify genetic variations that are thought to have an impact on different production traits or things like disease resistance (e.g., bovine mastitis). GATK is a popular tool for this sort of thing.

Genome assembly, i.e., the reconstruction of the genome, is another type of analysis that can be facilitated with long read assemblers like Falcon or short-read assemblers like SPAdes. Keep in mind, numerous well curated bovine genomes already exist (see The Bovine Genome Database), so your decision to do this will depend on the objectives of your study.

Hope this helps!

[Umer]

Hey, I've ready pervious published data. One majore process all of them apply is the Variant Calling pipeline. Different way but same objective.

Finding association of SNPs and Indels with production traits and GWAS studies require phenotypic data access which i do not have access to. So far i was only able to perform SNP/Indels calling through WGS data, annotation and enrichment analysis. Other thing i read about was predicting the effects of these polymorphisms with tools like SIFT, Provean etc.

Genome assembly part is something that will require alot of time and resources which currently i don't have so I didn't took that as an option to perform analysis.

These are the only two options for analyzing WGS data ? Thank You for your responce.