'\" t
.\"     Title: khmer
.\"    Author: [see the "AUTHOR(S)" section]
.\" Generator: Asciidoctor 2.0.12
.\"    Manual: \ \&
.\"    Source: \ \&
.\"  Language: English
.\"
.TH "KHMER" "1" "" "\ \&" "\ \&"
.ie \n(.g .ds Aq \(aq
.el       .ds Aq '
.ss \n[.ss] 0
.nh
.ad l
.de URL
\fI\\$2\fP <\\$1>\\$3
..
.als MTO URL
.if \n[.g] \{\
.  mso www.tmac
.  am URL
.    ad l
.  .
.  am MTO
.    ad l
.  .
.  LINKSTYLE blue R < >
.\}
.SH "NAME"
khmer \- k\-mer counting, filtering and graph traversal FTW!
.SH "SYNOPSIS"
.sp
.if n .RS 4
.nf
.fam C
khmer `<prog_name>` [options] <args>
.fam
.fi
.if n .RE
.sp
eg.
.sp
.if n .RS 4
.nf
.fam C
khmer `load\-into\-counting` \-x 1e8 \-k 20 reads.ct reads.fa.gz
.fam
.fi
.if n .RE
.SH "USAGE"
.sp
This manpage only describes the \f(CRkhmer\fP 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/" "" "."
.sp
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
\f(CRload\-into\-counting.py ...whatever...\fP you need to prefix this command with
\f(CRkhmer\fP.  Furthermore, the .py extension may be omitted, resulting in a
command of the format shown above.
.sp
If you don\(cqt like this, simply add /usr/lib/khmer/bin to your personal PATH.
.SH "AUTHOR"
.sp
This wrapper and manpage were written by Tim Booth, who takes no credit for
khmer itself.