The best pipeline for SNP calling in aquaculture breeding

Question

[zizigolu]

Hi,

I googled for the best practice for SNP detection in de-nono assembled fish genome further constracting SNP chip of verified SNPs. however among many methods and without a reference genome I am mixing up. do you have any suggested pipeline in this regard?

thank you

Answer 1

[ivivek_ngs]

The links in the below 2 papers should help you with a starting point. Take a look at them

link1

link2

This biostar post should also be insightful Also take a look at this paper and the pipelines of STACK and UNEAK

I think you have enough reference point to start with. Good luck!

[zizigolu]

Thabk you so much

I was invited to an interview and asked to present a suitable pipeline for developing SNP chips in fish by Skype but unfortunately I was rejected after selection process. however I will study what you suggested. thanks again

[ivivek_ngs]

As long as it helps am glad but I wonder why such questions in an interview unless they have an idea of how a de novo assembly is done. There is a difference between de novo assembly and SNP calling. First of all the motivation needs to be clear what is the question for when such Skype interviews are asked. Ideally, if you are aware of how de novo assembly work then you can always make a short presentation but then again these are not a good way to judge someone. Sorry, it's my opinion. If it's for an industry job I can still understand the motivation for such interviews but not in academia.

[zizigolu]

you absolutely correct, I did not mention about full presentation. I presented de novo assembly of percidae fishes then SNP calling finally constructing SNP chips for future breeding. in first Skype interview group leaders only asked about my CV and so on but in second interview project leader asked me to present my suggested pipeline for pottential PhD thesis in which I failed.