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.
My question is: What are the softwares that you recommend me to assemble these genomes (the largest has almost 8 Mbp)?
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.
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).
Thanks in advance.