The need for speed – making sense of the next generation of genome sequence data

The next-generation of sequencing technologies have greatly reduced the
time needed to sequence a eukaryotic genome from seven years for the
original human genome, to a matter of months, weeks or even days.
Handling the resulting flood of genome data requires similar advances
in software. In this month’s issue of Genome Biology, Ben Langmead and colleagues introduce Bowtie, open-source sequence assembly software which offers a dramatic advance in performance compared to earlier tools.

Previously published computational methods for assembling the human genome typically took several weeks to align sequence data for a new human genome sequence to the reference genome. The world’s fastest sequencing facilities can generate data faster than this, making the assembly process a bottleneck. Bowtie, which can generate an assembled
sequence from 14x sequencing coverage of the human genome in a matter of hours, is a significant advance in tackling this problem.

In his minireview highlighting the publication of this software, Paul Flicek from the EBI discusses the ‘need for speed’ in the approaching post-post-genomic era, where the generation of petabytes of sequencing data will become the norm and researchers and clinicians will expect require results in hours, not days or weeks.  Bowtie is able to handle the task of aligning next-generation genome sequence data to a reference genome in a manageable and usable time-frame. At Genome Biology, we eagerly anticipate the advances in biological understanding that next-generation sequencing technologies can deliver when combined with computational advances such as Bowtie.

Read the full article from Ben Langmead and colleagues on the Genome Biology website. The Bowtie software is open-source and can be downloaded from sourceforge.

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