Pacific Biosciences of California Inc (PACB)

[Paulieme]

Jan 14, 2014-- De novo assembly of complex genomes
using single molecule sequencing,
Michael Schatz Summary
• Long read sequencing of eukaryotic genomes is here
• Recommendations
< 100 Mbp: HGAP/PacBio2CA @ 100x PB C3-P5
expect near perfect chromosome arms
< 1GB: HGAP/PacBio2CA @ 100x PB C3-P5
expect high quality assembly: contig N50 over 1Mbp
> 1GB: hybrid/gap filling
expect contig N50 to be 100kbp – 1Mbp
> 5GB: Email [e-mail]
• Caveats
– Model only as good as the available references (esp. haploid sequences)
– Technologies are quickly improving, exciting new scaffolding technologies---- http://schatzlab.cshl.edu/presentations/2014-01-14.PAG.Single%20Molecule%20Assembly.pdf