Problem:

Today a colleague of mine asked the following question:

" Assuming I need to build from 0, a chromosome of a fish, with short reads but no other reference whatsoever [de novo assembly]:

Question 1: how much work is that?

Question 2: Is there a generic software (like SAMtools) that will align the reads in a scaffold one can use?

Question3: Basically, given a reasonably clear pipeline in terms of software, is it still blood sweat and tears or is it just a matter of getting it on a cluster?"

Very grateful for any suggestions, sources of information, software etc.