Hands-On Assembly of DNA Sequencing Reads as a Gateway to Bioinformatics

• Main Author: Paul Anthony Jensen
• Format: Article
• Language: English
• Published: American Society for Microbiology 2017-09-01
• Series: Journal of Microbiology & Biology Education
• Subjects: bioinformatics; genome assembly; DNA sequencing; genomic medicine
• Online Access: http://jmbesubmissions.asm.org/index.php/jmbe/article/view/1295

The scale of genomic sequencing data and the complexity of bioinformatic algorithms make it difficult for students to develop a concrete understanding of assembling complete genomes from millions of short DNA sequences. We present a hands-on activity where students explore the genome assembly process using short DNA sequences printed on paper. Topics highlighted during the lesson include overlap identification, reference sequences, and the challenges arising from sequencing errors, low-frequency mutations, and repetitive regions. Sample materials provide reads and solutions for assembling clinically relevant regions of the S. gordonii penicillin binding protein and the human HTT gene. An online tool allows instructors to generate custom read sets from other DNA sequences.