Editing BioMicroCenter:PacBio (section)

== APPLICATIONS ==
There are several applications for which PacBio sequencing are well suited (and many it is not!). The major ones are below:
=== [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.

=== [http://www.pacb.com/applications/target/index.html AMPLICON / RESEQUENCING] ===
PacBio reads can also be used to looks for variants in specific regions. The long reads allow for better detection of large rearrangements and understanding repetitive regions of the genome. <BR><BR>
The use of long reads in assembly can also establish phasing of mutations. Short reads will typically not be able to span multiple mutations on a single read. PacBio reads are long enough to enable detection of multiple mutations as coming from the same strand. <BR><BR>
Indexing is possible with resequencing amplicons but indexes should be added during PCR and not during library preparation.

=== [https://www.pacb.com/applications/rna-sequencing/ WHOLE TRANSCRIPT] ===
Unlike short read RNAseq, which requires fragmenting of the RNA, full length cDNAs can be sequenced on the PacBio Sequel. This allows direct detection of different splice isoforms. The low number of reads makes using this as a counting method challenging.

=== [http://www.pacb.com/applications/base_modification/index.html BACTERIAL BASE MODIFICATION] ===
One aspect that makes PacBio sequencing unique is its ability to recognize chemical modifications of bases. Because the instrument works by measuring the time a nucleotide is in the active site, it has an axis of “time”. Basepairing modified bases has different kinetics which allows the sequencer to provide a likelihood score that any given base has been modified. Methylcytosine, Hydroxymethylcytosine, 6-methyl adenosine and many others have been detected utilizing this kinetics mode.