<p>I have sequencing data of five bacteria, which were generated using Illumina MiSeq. Four of them were sequenced using a paired-end 2x300 protocol and one was sequenced using the nextera mate-pair protocol.</p>

<p>My question is: What are the softwares that you recommend me to assemble these genomes (the largest has almost 8 Mbp)?</p>

<p>I have access to a CLC Workbench. It seems quite ease to use, but I dont know if it is the best one. Most of papers that I found that evaluate the performance of assemblers from two-three years ago.</p>

<p>I also have to mention that I have two i7 with 8 threads PCs available for this objective (one with 32 and another with 8 Gb RAM).</p>

<p>Thanks in advance.</p>

<p>You should read in the literature to know which one is the best one for you specific data. Here you have a nice paper comparing some assembly tools, and it is a recent paper (2014): <a href="http://genomebiology.com/2014/15/3/R42">http://genomebiology.com/2014/15/3/R42</a><br />
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In my opinion SOAPdenovo2 and SGA are a good choice. Bambus is quite difficult to install and to understand. SPACE also is nice, but if you want to use the last version you have to pay so...<br />
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Hope it helps.</p>
