10.5061/DRYAD.4368H
Hebert, Paul D.N.
University of Guelph
Braukmann, Thomas W.A.
University of Guelph
Prosser, Sean W.J.
University of Guelph
Ratnasingham, Sujeevan
University of Guelph
deWaard, Jeremy R.
University of Guelph
Ivanova, Natalia V.
University of Guelph
Janzen, Daniel H.
University of Pennsylvania
Hallwachs, Winnie
University of Pennsylvania
Naik, Suresh
University of Guelph
Sones, Jayme E.
University of Guelph
Zakharov, Evgeny V.
University of Guelph
Data from: A sequel to Sanger: amplicon sequencing that scales
Dryad
dataset
2019
nucleotide composition
SMRT sequencing
homopolymer
2019-01-12T00:00:00Z
2019-01-12T00:00:00Z
en
https://doi.org/10.1186/s12864-018-4611-3
773653546 bytes
1
CC0 1.0 Universal (CC0 1.0) Public Domain Dedication
Although high-throughput sequencers (HTS) have largely displaced their
Sanger counterparts, the short read lengths and high error rates of most
platforms constrain their utility for amplicon sequencing. The present
study tests the capacity of single molecule, real-time (SMRT) sequencing
implemented on the SEQUEL platform to overcome these limitations,
employing 658 bp amplicons of the mitochondrial cytochrome c oxidase I
gene as a model system. By examining templates from more than 5,000
species and 20,000 specimens, the performance of SMRT sequencing was
tested with amplicons showing wide variation in GC composition and varied
sequence attributes. SMRT and Sanger sequences were very similar, but SMRT
sequencing provided more complete coverage, especially for amplicons with
homopolymer tracts. Because it can characterize amplicon pools from 10,000
DNA extracts in a single run, the SEQUEL reduces costs 40-fold from Sanger
analysis. Reflecting the capacity of each instrument to recover sequences
from more than five million DNA extracts a year, this platform facilitates
massive amplicon characterization.
CCSReads_DS-PBBC1Sequel CCS reads for 99%, 99.9%, and 99.99% partitions of
data set DS-PBBC1.CCSReads_DS-PBBC2Sequel CCS reads for 99%, 99.9%, and
99.99% partitions of data set DS-PBBC2.CCSReads_DS-PBBC3Sequel CCS reads
for 99%, 99.9%, and 99.99% partitions of data set
DS-PBBC3.CCSReads_DS-PBBC4Sequel CCS reads for 99%, 99.9%, and 99.99%
partitions of data set DS-PBBC4.mBRAVE_DS-PBBC1mBRAVE output for data set
DS-PBBC1.mBRAVE_DS-PBBC2mBRAVE output for data set
DS-PBBC2.mBRAVE_DS-PBBC3mBRAVE output for data set
DS-PBBC3.mBRAVE_DS-PBBC4mBRAVE output for data set DS-PBBC4.