Forum: Bob Harris of the LASTZ aligner uses this
12
gravatar for Istvan Albert
4.4 years ago by
Istvan Albert ♦♦ 79k
University Park, USA
Istvan Albert ♦♦ 79k wrote:

Dr. Bob Harris' journey to bioinformatics may be more circuitous than that of others in the field. He received his Bachelor’s degree in Applied Mathematics from Carnegie-Mellon University in 1979 then went on to work in industry as a programmer, mostly in embedded systems. In the early 1980s he was writing games for console video game systems. He had successes with games such Killer Bees and  WarRoom, this latter was declared the "most innovative game" of 1984. In the late 1980s he switched to digital image processing, and in the mid 1990s moved into digital television equipment. His accomplishments include implementing a hardware-assisted scientific imaging system called NuVision and a fault-tolerant MPEG audio/video encoding card used in broadcast television systems.

Along the way he received his Master’s degree in Computer Science from the University of Tennessee in 1993 then, in 2003 entered the Ph.D program at Penn State in the group of Webb Miller (of Blast fame). He graduated in 2007 with a thesis on LASTZ one of the most commonly used general pairwise alignment tools.

LASTZ is a tool with a long history and pedigree that goes back to the beginning of bioinformatics. Its functionality and usage patterns have been polished over the years, tuned and refined by thousands of users and just as many use cases,  integrated into data services at UCSS and Ensemble. LASTZ  is most likely the aligner that allows for the most options for data formats: a staggering number of input and outputs types and customizations, supports a wide variety of options, and performs admirably on a wide variety of tasks from whole genome alignments to short read mapping.

With the advent of longer,more error prone sequencing such as that produced by MinION, aligners such as LASTZ may see a resurgence in their utility and popularity.


What hardware do you use?
I use a 10 year old Mac for editing and as a portal to the linux-based machines where all the computation is performed. Those machines have many cores and oodles of memory; sometimes in a batch cluster configuration, sometimes not.

What is your text editor?
TextWrangler, because I'm able to configure it to match the behavior of some editor I was using 20 years ago.

What software do you use for your work?
I do a lot of read mapping and alignment. For some projects I use bwa, for others I use lastz. I use blat and ncbi-blast, mostly for consistency checks.

What do you use to create plots and charts?
R, though the relearning curve is a serious bummer. In some cases I've written my own python scripts to create svg.

What do you consider the best language to do bioinformatics with?
Whatever language the user is most comfortable with. For me it's a combination of python and C, and some shell scripting as glue. A decade ago I had a choice of learning perl or python. I chose perl and spent six months using it but it never "clicked" for me. Then I tried python and I haven't looked back.

What bioinformatics tools/software do not get enough recognition?
Tools that do sequencing error correction. I don't have a specific tool in mind (hammer comes to mind but there should be better ones now).


See all post in this series https://www.biostars.org/t/uses-this/

To be notified of new post in the series follow the first post: Jim Robinson of the Integrative Genomics Viewer (IGV) uses this

uses-this forum • 2.3k views
ADD COMMENTlink modified 4.4 years ago • written 4.4 years ago by Istvan Albert ♦♦ 79k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1208 users visited in the last hour