---
name: "khmer"
section: "1"
platform: "linux"
package: "khmer"
version: "3.0.0~a3+dfsg-4+b2"
release: "Debian 12 (Bookworm)"
platforms: ["linux"]
url: "https://new.carta.tech/khmer"
---

# khmer(1)

k-mer counting, filtering and graph traversal FTW!

## NAME

khmer - k-mer counting, filtering and graph traversal FTW!

## SYNOPSIS

```
khmer `<prog_name>` [options] <args>
```

eg.

```
khmer `load-into-counting` -x 1e8 -k 20 reads.ct reads.fa.gz
```

## USAGE

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  \<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.

## AUTHOR

This wrapper and manpage were written by Tim Booth, who takes no credit for khmer itself.