<p>I installed ABySS following the instructions from the <a href="https://github.com/bcgsc/abyss#install-abyss-on-debian-or-ubuntu">official documentation</a>.</p>

<pre>
&gt;sudo apt-get install abyss</pre>

<p>and then proceeded with a simple test</p>

<pre>
&gt;wget http://www.bcgsc.ca/platform/bioinfo/software/abyss/releases/1.3.4/test-data.tar.gz
&gt;tar xzvf test-data.tar.gz
&gt;abyss-pe k=25 name=test in=&#39;test-data/reads1.fastq test-data/reads2.fastq&#39;</pre>

<p>Everything looks fine except when I run</p>

<pre>
&gt;abyss-fac test-unitigs.fa
abyss-fac: command not found</pre>

<p>It seems that the only avaiable command is abyss-pe.<br />
Any idea of what could be the problem?</p>

If you look at [the Debian package page][1], the only thing installed to `/usr/bin` is `abyss-pe`, which is why you can find it from the command line. Try:

    /usr/lib/abyss/abyss-fac test-unitigs.fa

 [1]: https://packages.debian.org/wheezy/amd64/abyss/filelist