Auto Sequencer: A DNA Sequence Alignment and Assembly Tool

Abstract

The process of determining the exact order of nucleotides in DNA is a crucial component of a wide variety
of research applications known as DNA sequencing. Over the last fifty years, several DNA sequencing
technologies have been well characterized through their nature and the kind of output they provide. Even
with significant advances in DNA sequencing technology, sequencing and assembly of large pieces of
DNA remains a complex task. It requires sequencing small reads of DNA at a time, and performing DNA
sequence assembly to merge the individual pieces into a single contiguous sequence. DNA sequence
assembly, albeit tedious and time consuming, is a process in which short DNA sequence fragments are
merged into longer fragments in the attempt to reconstruct the original DNA sequence. This is usually
achieved by manually identifying sequence overlaps between two reads before aligning them into
one contiguous sequence. Then, with the aid of online tools or software, this contiguous sequence is
translated into protein sequence. While this process may only take a few minutes, the complexity of
sequence translation and assembly can be driven by two major challenges: finding the most reasonable
overlap in sequences that may contain repeats or low quality regions, and outputting both nucleotide
and protein sequence in an easy to use, comprehensive output. To facilitate this process, we introduce
an all-in-one tool: Auto Sequencer. This user-friendly tool can combine and translate raw DNA sequence
files by finding the most reasonable overlap between them displaying outputs in flexible formats.