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 varietyof research applications known as DNA sequencing. Over the last fifty years, several DNA sequencingtechnologies have been well characterized through their nature and the kind of output they provide. Evenwith significant advances in DNA sequencing technology, sequencing and assembly of large pieces ofDNA remains a complex task. It requires sequencing small reads of DNA at a time, and performing DNAsequence assembly to merge the individual pieces into a single contiguous sequence. DNA sequenceassembly, albeit tedious and time consuming, is a process in which short DNA sequence fragments aremerged into longer fragments in the attempt to reconstruct the original DNA sequence. This is usuallyachieved by manually identifying sequence overlaps between two reads before aligning them intoone contiguous sequence. Then, with the aid of online tools or software, this contiguous sequence istranslated into protein sequence. While this process may only take a few minutes, the complexity ofsequence translation and assembly can be driven by two major challenges: finding the most reasonableoverlap in sequences that may contain repeats or low quality regions, and outputting both nucleotideand protein sequence in an easy to use, comprehensive output. To facilitate this process, we introducean all-in-one tool: Auto Sequencer. This user-friendly tool can combine and translate raw DNA sequencefiles by finding the most reasonable overlap between them displaying outputs in flexible formats.