Bioinformatics Workflow

Question

[SibabalweKula]

Hi everyone

I am doing bioinformatics and computational biology Thesis project on genetic Characterisation of Plant Clones to a reference genome. The aims are to Read map all clones to the reference genome, Identify accumulated somatic mutations over time, compare all the 20 clones with each other to identify inter-clone genetic variability and, hopefully at the end to possibly link their role to the possible phenotypic difference in clones. I am working with Illumina short-reeds.

Any suggested workflows, importantly tools that I can use to carry out a comprehensive assessment of the aims?

My proposed workflow is, align all clones to the reference genome (BWA), Flagstat for mapping information, GATK for variant annotation, then I need tools for interpretation of the results.

I also want a way in which I can compare a set of 12 clones to 8 clones, to potentially link the mutations that are present between the types. The hypothesis is that the 18 clones were derived from the 12 initial clones at a later stage. Please assist with useful steps that I can follow for accomplishment of a good research study?

Answer 1

[jared.andrews07]

Generally, people use tools specifically geared towards comparative genomics for these types of studies, rather than aligning each individually and manually trying to compare them. Googling "comparative genomics" will get you started, and tools like cactus may get you a large part of the way towards your goal.