<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>

For bacterial genome, [GAGE-B paper][1] (2013) compare 8 genome assemblers:

 - ABySS v1.3.4
 - CABOG v7.0
 - MIRA v3.4.0
 - MSRCA v1.8.3
 - SGA v0.9.34
 - SOAPdenovo2 v2.04 + GapCloser v1.12
 - SPAdes v2.3.0
 - Velvet v1.2.08

All GAGE-B data and assembly recipe are available [here][2].

For more recent comparison of genome assemblers, have a look [here][3].

As each bacteria genome size and GC% is different, you need to check [these reproducible Benchmarks][4].

 [1]: http://bioinformatics.oxfordjournals.org/content/29/14/1718
 [2]: http://ccb.jhu.edu/gage_b/index.html
 [3]: http://nucleotid.es/
 [4]: http://nucleotid.es/benchmarks/