We chatted with Dr. Luke Daum, Chief Scientific Officer at Longhorn Vaccines and Diagnostics about his work with Mycobacterium tuberculosis.
Tell us about your work!
Currently, we do a lot work in Africa with specific focus on Mycobacterium tuberculosis (MTB) detection and next-generation sequencing (NGS). We develop molecular reagents and products that simplify and enhance molecular detection from the point of sample collection, detection, and DNA sequencing. We also do work with influenza viruses and have recently done some whole-genome MRSA sequencing as well.
How has DNASTAR software helped you with your research goals?
In 1999, I established the U.S. Air Force’s molecular influenza strain surveillance program and was first introduced to DNASTAR by the CDC. Since then, I’ve never let go. I prefer DNASTAR over other bioinformatics software because it’s so simple to use. I have observed and participated in the evolution and maturation of DNASTAR software from simple gene alignments of DNA off automated slab gel sequencers to today’s cutting edge, multimillion read NGS assemblies! DNASTAR continues to mature alongside rapid advances in sequencing technologies.
What does DNASTAR software do best, in your opinion?
Since we do a lot of barcoding/indexing of patient isolate samples, I like the ease with which I can perform a multi-patient analysis within a single SeqMan NGen assembly-the software enables you to quickly switch within barcoded/indexed patients. I also like that with SeqMan NGen I can quickly input a reference gene or gene panel of interest against a full genomic library file to quickly assess for mutations in genes of interest. Sometimes you just want to look at specific genes and you don’t always need/want the hassle of dealing with an entire 4.2 million bp MTB genome!
Can you speak to DNASTAR’s support for you and your work?
The DNASTAR team works closely with Life Technologies and Illumina to simplify the analysis of NGS data for the everyday scientist. Most scientists are good at empirical experimentation and molecular biology testing but a bit intimidated by the size of raw data output and the bioinformatics aspects of NGS. DNASTAR bridges the gap between 2-3 gigabytes of raw NGS sequence data and a thorough genetic analysis containing graphical alignments, mutational reports, and phylogenies. For example, from incredibly large raw MiSeq data files containing 24 indexed MTB genomes I can easily use the tools in DNASTAR to assemble contigs and analyze TB isolates for mutations in antibiotic resistance genes. From here it’s simple to generate SNP reports, multiple sequence alignments, and phylogenetic trees.
Is there anything else you’d like to share with us?
When I get into trouble I find it easy to contact DNASTAR technical support. Matthew Keyser and his team are always available for troubleshooting and resolving user issues.