Technological advances in DNA sequencing over the last decade now permit
the production and curation of large genomic datasets in an increasing
number of non-model species. Additionally, this new data provides the
opportunity for combining datasets, resulting in larger studies with a
broader taxonomic range. Whilst the benefits of new sequencing platforms
are obvious, shifts in sequencing technology can also pose challenges
for those wishing to combine new sequencing data with data sequenced on
older platforms. Here, we outline the types of studies where the use of
curated data might be beneficial, and highlight potential biases that
might be introduced by combining data from different sequencing
platforms. As an example of the challenges associated with combining
data across sequencing platforms, we focus on the impact of the shift in
Illumina's base calling technology from a four-channel to a two-channel
system. We caution that when data is combined from these two systems,
erroneous guanine base calls that result from the two-channel chemistry
can make their way through a bioinformatic pipeline, eventually leading
to inaccurate and potentially misleading conclusions. We also suggest
solutions for dealing with such potential artifacts, which make samples
sequenced on different sequencing platforms appear more differentiated
from one another than they really are. Finally, we stress the importance
of archiving tissue samples and the associated sequences for the
continued reproducibility and reusability of sequencing data in the face
of ever-changing sequencing platform technology.