title: Whole genome sequencing of B. ovatus ATCC 8483 using the PacBio RSII platform
design: High molecular weight genomic DNA was extracted from an overnight culture using a hexadecyltrimethylammonium bromide (CTAB)/chloroform-isoamyl alcohol genomic DNA extraction protocol and then sheared to 10-20 kb fragments using Covaris g-TUBES. Sequencing libraries were prepared with 5 μg of the sheared DNA according to the “20 kb Template Preparation with 15kb Cutoff Using BluePippin™ Size-Selection” protocol (https://pacbio.secure.force.com/Share/Protocol?id=a1q70000004GlScAAK) and run on the Pacific Biosciences RSII sequencer with 240 minutes movies and the P6/C4 chemistry. Two Single Molecule Real Time (SMRT) cells were used, yielded 103,157 reads and 1,107 MB of sequence data. Reads were assembled using PacBio’s hierarchical genome-assembly process (HGAP) 2.0. Polymerase reads with quality score lower than 0.80 were filtered and remaining high quality reads were processed into subreads by removing adaptor sequences. Subreads longer than 500 bp were retained as input for the HGAP assembler with subreads longer than 4kb treated as seeds. The error-corrected pre-assembled reads were used with the Celera Assembler to produce a single large linear contig 6,491,858 bp in length which after finishing and correction with Illumina 100 bp paired end reads from a Nextera V2 library run on a MiSeq V2 instrument resulted in a genome of 6,472,489 bp.
identifiers.namespace: Washington University in St. Louis
identifiers.id: B. ovatus ATCC 8483, PacBio RSII