was comparable to an assembly constructed using 100x paired-end Illumina reads. The N50 for the corrected PBcR data was also longer than the Illumina data (4.65MBp compared to 3.32 Mbp for the Illumina reads). A similar trend was seen in the sequencing of the Escherichia coli JM221 genome: a 25x PBcR assembly had a N50 triple that of 50x 454 assembly. Automated finishing of bacterial genomes This study employed two different methods for hybrid genome assembly: a scaffolding approach that supplemented currently available sequenced contigs with PacBio reads, as well as an error correction approach to improve the assembly of bacterial genomes. The first approach in this study started with high-quality contigs constructed from sequencing reads from second-generation (Illumina and 454) technology. These contigs were supplemented by aligning them to PacBio long reads to achieve linear scaffolds that were gap-filled using PacBio long reads. These scaffolds were then supplemented again, but using PacBio strobe reads (multiple subreads from a single contiguous fragment of DNA ) to achieve a final, high-quality assembly. This approach was used to sequence the genome of a strain of Vibrio cholerae that was responsible for a cholera outbreak in Haiti. This study also used a hybrid approach to error-correction of PacBio sequencing data. This was done by utilizing high-coverage Illumina short reads to correct errors in the low-coverage PacBio reads. BLASR (a long read aligner from PacBio) was used in this process. In areas where the Illumina reads could be mapped, a consensus sequence was constructed using overlapping reads in that region. One area of the genome where the use of the long PacBio reads was especially helpful was the ribosomal operon. This region is usually greater than 5kb in size and occurs seven time throughout the genome with an average identity ranging from 98.04% to 99.94%. Resolving these regions using only short second generation reads would be very difficult but the use of long third generation reads makes the process much more efficient. Utilization of the PacBio reads allowed for unambiguous placement of the complex repeated along the scaffold. Using only short reads This study employs a hybrid genome assembly approach that only uses sequencing reads generated using SOLiD sequencing (a second-generation sequencing technology). The genome of C. pseudotuberculosis was assembled twice: once using a classical reference genome approach, and once using a hybrid approach. The hybrid approach consisted of three contiguous steps. Firstly, contigs