Editing BioMicroCenter:PacBio (section)

=== [http://www.pacb.com/applications/denovo/  DE NOVO ASSEMBLY / LARGE SCALE MAPPING] ===
Assembly is the biggest strength of PacBio. While the individual base error rate is quite high (~14%), the errors are random and so resequencing rapidly lowers the error rate. Using only PacBio reads, 60x coverage can give very good assembly – typically completing genomes in 1 shot . A 4 Mbp genome can be done on a single SMRT cell. <BR><BR>
A second strategy is to use PacBio reads to supplement short reads and join scaffolds.  Here, standard short reads make up the bulk of the assembly but the separate scaffolds can be spanned by PacBio reads. 7x reads has been the convention for this type of sequencing. 400 Mbp of genomic DNA can be done on a single SMRT cell. Indexing cannot be done easily with PacBio samples - particularly long reads - and so the 'quanta' for SMRTcells should be considered as up to three genomes per SMRTcell.