Diversity Study Using Illumina For Non Model Species Having Highly Repetitive And Complex Genome

Question

[Abhishek]

How can I utilize the power of next generation sequencing (Illumina) for diversity study in polyploid plants for which there is no reference genome. What are its various steps.

Answer 1

[2184687-1231-83-]

You can do whole genome sequencing with Illumina for a variety of diverse samples at relatively low-coverage. Then assemble all the sequencing data together in one go, combining all samples together in the input data for the assembler, in order to have long contigs with average high-coverage to define the reference genome. Then map back the reads of each sample separately to the reference contigs in order to identify the SNPs present in each of your samples. Then analyse the SNPs for measures like FST and similar.

Answer 2

[SES]

Step 1) I think you should start by typing your keywords in a search engine like Google, or better yet, an academic search engine like PubMed or Web of Science.

Step 2) Read the relevant papers you find and develop some specific questions once you have a better understanding of your proposed study.

If you still have questions after searching the internet and reading papers then,

Step 3) Ask a specific question on a specialized website, listserv, or blog.

Here is a guide for how to go about step 3 (this is programming-related but the general rules apply): How to ask questions the smart way.

And note that, "how to go about a diversity study?" is not a good question for many reasons.

[Michael]

unfortunately this answer is not very helpful either, it is true that the question is a bit unspecific but so is the answer. It is better to put such criticism into a comment.

[SES]

How is the answer unspecific? It is a step by step approach, maybe not delivered perfectly, but I meant it to be helpful. The OP would learn much more by doing some basic searches and reading than filtering through the answers that a vague question will generate. Also, I think it is more helpful to ask for someone to rethink a question, and respect others, rather than posting an answer that may not be relevant. Maybe you disagree, but this is laid out on the "ask a question" page of this site (follow the 10 rules link: http://biostar.stackexchange.com/questions/ask).