The MiSeq Desktop Sequencer was added to CAT-AgroFood’s Next Generation Sequencing facility in February 2014. This purchase allows for sequencing 300 base pair long read lengths and gives maximum flexibility using nano, micro or normal scalable runs. The MiSeq’s short nano run takes less than six hours. The longest run is 65 hours, during which it sequences up to 15 gigabases.
MiSeq is faster, HiSeq is cheaper
“The MiSeq is a great addition to the HiSeq”, said Gabino Sanchez Perez, genomics & bioinformatics specialist at Wageningen UR, who ran his first samples soon after the machine was installed. The most important advantage, according to Sanchez Perez, is that by making use of the 300 bp paired end reads of the MiSeq we can create merged reads that are five times longer than the reads of the HiSeq: up to 550 base pairs long. The HiSeq, on the other hand, has a better “price per base”.
Throughput or targeted application?
The HiSeq sequences up to 300 gigabases in one run. This run, however, usually takes twelve days. Sanchez Perez: “So what do you do in the meantime? You use the MiSeq for targeted applications.” And he sees other good possibilities to combine the HiSeq and MiSeq. It can happen that samples are contaminated. This will only become apparent after they have been sequenced. So before starting a twelve day run in the HiSeq, it would be wise to first check the samples for contamination in the MiSeq, Sanchez Perez suggests. This check is done in a matter of hours.
The MiSeq is particularly suited for projects that benefit from a larger read, like any de-novo genome sequencing, metagenomics or amplicon sequencing as well as for QC purposes to streamline large HiSeq sequencing projects.