Publication Date:
2019-07-16
Description:
In April 2012, your journal published a
study by Loman et al.1 that systematically
compared desktop next-generation
sequencers (NGS) from three instrument
providers. Using the custom scripts supplied
by the authors, the same software and the
same draft genome (with 153 remaining gaps
within several scaffolds) as the reference,
we reproduced their results with their data
of the enterohemorrhagic Escherichia coli
(EHEC) strain found in the 2011 outbreak in
Germany. However, we wish to bring readers’
attention to some shortcomings in the report
from Loman et al.1, focusing particularly on
its discussion of read-level error analysis.
NGS is a rapidly changing market, which
clearly complicates the comparisons such as
that made by Loman et al. Since the original
study1, Illumina (San Diego) has launched the
MiSeq sequencer officially and has released
Nextera library construction kits and 2 ×
250–base-pair (250-bp) paired-end (PE)
sequencing chemistry. Furthermore, Life
Technologies (Carlsbad, California), has made
200-bp and 300-bp kits available for the Ion
Torrent Personal Genome Machine (PGM).
Roche (Basel, Switzerland) has updated the
Sequencing System software for its 454 GS
Junior (GSJ) from version 2.6 to 2.7. In this
report, we provide an up-to-date snapshot of
how benchtop platforms have evolved since
the previous study1.
Repository Name:
EPIC Alfred Wegener Institut
Type:
Article
,
isiRev
Format:
application/pdf
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