Although BLAST (Basic Local Alignment Search Tool) is not strictly a next generation sequencing tool, I use it regularly for a wide variety of tasks. Here are a few scenarios I use BLAST for:

• Finding similar regions to my region-of-interest (I know there are other ways to do this),
• Comparing two nucleotide sequences (again, I know there are other tools available),
• Checking primer specificity,
• Plus, I usually BLAST anything weird that I find during sequencing analysis (strangely mapped reads, consensus sequences around unusual variants, targeted regions with no coverage, etc.).

I usually use the “original” NCBI BLAST. NCBI provides extensive documentation (there’s even a chapter about it in the NCBI Handbook and you should check out the Help page as well).  Other than the standard “nucleotide sequence query against nucleotide database” there are several different versions of BLAST available, like protein blast and different versions of translated nucleotide queries. There are also some specialized BLAST versions, like Primer BLAST, pairwise sequence alignment by BLAST,  etc. BLAST can also be used as a standalone command line tool.

NCBI is not the only webpage/database that has a BLAST search avaliable:

• The EBI webpage has a BLAST function too. With this version you can search in the HLA allele database and the patented sequence database as well.
• Ensembl also has a BLAST (or BLAT) search function.

For other available BLAST versions, see here.