What is the difference between the following two commands?
sort -u FILE
sort FILE | uniq
Using sort -u does less I/O than sort | uniq, but the end result is the same. In particular, if the file is big enough that sort has to create intermediate files, there's a decent chance that sort -u will use slightly fewer or slightly smaller intermediate files as it could eliminate duplicates as it is sorting each set. If the data is highly duplicative, this could be beneficial; if there are few duplicates in fact, it won't make much difference (definitely a second order performance effect, compared to the first order effect of the pipe).
Note that there times when the piping is appropriate. For example:
sort FILE | uniq -c | sort -n
This sorts the file into order of the number of occurrences of each line in the file, with the most repeated lines appearing last. (It wouldn't surprise me to find that this combination, which is idiomatic for Unix or POSIX, can be squished into one complex 'sort' command with GNU sort.)
There are times when not using the pipe is important. For example:
sort -u -o FILE FILE
This sorts the file 'in situ'; that is, the output file is specified by -o FILE, and this operation is guaranteed safe (the file is read before being overwritten for output).