PacBio machine in Wageningen ‘among the best performing in the world’

Published on
April 11, 2014

CAT-AgroFood’s third generation sequencer PacBio RS II is performing better than ever before. Since it was upgraded from RS I to RS II and supplied with a new chemistry kit in the summer of 2013, the throughput has doubled and the read length has massively increased. “It is now one of the best PacBio’s in the world, delivering the longest read lengths amongst the existing service providers”, says Gabino Sanchez Perez. In Wageningen the PacBio is used to sequence tomato, melon, animal, fungal and microbial genomes.

Reads of 30,000 base pairs

Where the Illumina HiSeq sequences fragments of up to 100 base pairs, the PacBio RS II produces reads with an average of 8,000 base pairs, and can even produce reads of up to 30,000 base pairs. Hence, it becomes much easier to locate the position of base pairs and piece the genome puzzle together.

The PacBio is known to have an error rate of 15 per cent. “But the good thing is that the errors are absolutely random, so if you read a sample three times you can eliminate almost all errors”, explains Sanchez Perez.

Blue Pippin makes PacBio even more useful

To get the most out of the PacBio RS II, CAT-AgroFood also purchased a Blue Pippin for preparing higher quality libraries. This instrument selects genome fragments according to size. To make sure that only the long fragments will be subsequently sequenced by the PacBio, which gives much more useful results.