This is not so much a question of HOW, but more of a question of "is it worth the hassle?".
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]:
- how much work is that?
- Is there a generic software (like SAMtools) that will align the reads in a scaffold one can use?
- 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 (papers), software etc.