<p>I have a set of paired end and single end MiSeq Illumina reads: <code>Sample_1.fastq, Sample_2.fastq, Sample_s.fastq</code></p>

<p>If I wanted to assemble this with Abyss it would be:</p>

<pre>
abyss-pe K=Kmer name=Sample_Kmer in=&#39;Sample_1.fastq Sample_2.fastq&#39; se=&#39;Sample_s.fastq&#39;</pre>

<p>Now I want to perform a hybrid assembly with pacbio reads thrown into the mix. I have 3 PacBio subreads: <code>Sample.1.subreads.fastq, Sample.2.subreads.fastq, Sample.3.subreads.fastq</code> (all ~2 gigabytes)</p>

<p>My question is, how do I include all of these read files in one assembly command?</p>

<p>I was able to do this in Spades/Soapdenovo so far.</p>

<p>I think Abyss will not use long reads on the assembly step, it will only use long reads for scaffolding - check on its <a href="https://github.com/bcgsc/abyss#rescaffolding-with-long-sequences">manual</a>. <a href="http://sourceforge.net/projects/ceruleanassembler/">Cerulean</a> performs hybrid assembly starting from an Abyss assembly, but it is designed for small genomes.</p>
