PacBio Achieves 500Mb/SMRT Cell Throughput in Newly Released Human Data
October 22nd, 2013- PacBio Achieves 500Mb/SMRT Cell Throughput in Newly Released Human Data
In collaboration with Evan Eichler (Howard Hughes Medical Institute, University of Washington), we sequenced CHM1TERT, a well-studied cell line derived from a complete hydatidiform mole (CHM). A hydatidiform mole is defined as a pregnancy with no embryo and clinically presents in approximately 1 in 1,500 pregnant women in North America. The CHM cells have a diploid genome, typically XX, that is a result of replication of a haploid paternal (sperm) genome. Through the corresponding absence of allelic variation, this sample has been used to generate a haploid reference genome sequence, and many associated resources are available, including physical maps, genotypes (iSCAN), and a large-insert BAC library (CHORI-17). It is also one of the targets for the production of a higher quality “platinum” genome assembly.
The stats are quite fascinating. They have 66 SMRT cells producing 32,559,803,198 bases of post-filtered nucleotides. Therefore, on average, each SMRT cell produced 493Mb of sequences. A few days back, we asked about the typical throughput of PacBio machines at seqanswers. Lex Nederberg and Genomax reported 150-300 Mb with pre-P4 chemistry and only one exceptional case of 730 Mb with P4 chemistry. On the other hand, 500 Mb per SMRT cell appears to be common with P5-C3 chemistry here. Other stats:
Average read length: 8,849 bp
Half of sequenced bases in reads greater than: 10,985 bp
5% of sequenced DNA inserts longer than: 18,060 bp
Longest DNA insert sequenced: 41,460 bp
PacBio® RS II instrument time for sequencing: 10 days
Their blog post has informative charts on read size distribution and one example of a 114.2 kb deletion in the human genome !!!
(part 2 of 1) for link go to IHUB M B