Student Presenter(s): Helly S. Amin
Faculty Mentor: Bryan Gibb
Department: Life Sciences
School/College: College of Arts and Sciences, Long Island
The study focuses on the workflow of sequencing and analysis of the microbial genome. The Whole Genome Sequence (WGS) provides the most comprehensive map of an organism's genetic make-up. Intrinsic properties of the genome are not the only consideration before sequencing. The extraction of high-quality DNA is one such aspect that is of utmost importance. Recent advances in sequencing technologies and analysis tools have rapidly increased the output and analysis speed as well as reduced the costs of WGS. Emerging sequencing technology like Illumina sequencing allows rapid, cheap and accurate whole genome bacterial analyses, but short reads (<300 bp) do not usually enable complete genome assembly. Despite its many advantages in cost, run time, and output, the Nanopore technology system is still a technology under development due to its high error rate (∼10%) compared to Illumina (0.1%). The sequencing data is obtained in FASTQ form which needs to be converted into FASTA form for further analysis. The most common platform for genomic data analysis is a Linux Operating System, which consists of plenty of command line and graphical tools for assembling raw reads. From this assembled DNA sequence, tools can be applied for genome characterization. This characterization is achieved by determining the bacterial identity of the sample, annotating genes, and identifying genes of clinical importance, such as Antimicrobial Resistance (AMR) and virulence genes.