The difference is not in the focus as I think both cover very similar topics but in the way the sites approach content management.

Seqanwers is a traditional web forum where each post follows the other by creation date. There are no restrictions/recommendations on what each post may contain.

Biostar has a more structured content where questions, answers and comments are all different types of content. Moreover all posts are ranked by votes and thus the community can better express the value that they assign to it. At Biostar many dozens of people work on making posts better over long term, content is edited, re-tagged, titles reworded etc. I think from the point of view of information content Biostar is far more dense and much easier to find what you need.

Bioinformatics covers a lot more than just sequencing. BioStar embraces all. SeqAnswers embraces the sequencing. I still think for most NGS related questions you will be better served in the more specialist environment, not that there's anything wrong with the support for that topic here.

In addition to what Dan & Istvan said: occasionally, people are directed to SeqAnswers when they ask a question which is less to do with the bioinformatics of NGS and more to do with the molecular biology protocols.