khmer `<prog_name>` [options] <args>
khmer `load-into-counting` -x 1e8 -k 20 reads.ct reads.fa.gz
This manpage only describes the khmer wrapper script. To find out about the software and how to use it please see /usr/share/doc/khmer or else <URL: http://khmer.readthedocs.org/ >.
On Debian/Ubuntu, package maintainers avoid putting large collections of scripts directly into the system PATH. Rather, a single wrapper script is used to launch the script you want to use; therefore if the khmer instructions say to run load-into-counting.py ...whatever... you need to prefix this command with khmer. Furthermore, the .py extension may be omitted, resulting in a command of the format shown above.
If you don't like this, simply add /usr/lib/khmer/bin to your personal PATH.
This wrapper and manpage were written by Tim Booth, who takes no credit for khmer itself.