Brian Walenz

Software Engineer

Ten years is a long time to spend working on a problem, but Brian proudly admits that he has spent that long working on the DNA sequence read assembly problem. In that time, he has seen five new sequencing technologies introduced (there were certainly more that tried but they never gained significant presence). Each technology came with the promise of solving all assembly problems, only for us to painfully discover that each one introduced a new set of problems. As a result, each new technology required adjustments, or even entirely new algorithms, to handle their specific characteristics and systematic errors. This is why he is still doing read assembly after ten years. It is just one problem, but it changes every year.



A single molecule sequence assembler for genomes large and small

Celera Assembler PBcR

PacBio read correction and assembly pipeline [ retired ]
An improved genome assembly uncovers prolific tandem repeats in Atlantic cod
BMC Genomics, January 18, 2017
Tørresen OK, Star B, Jentoft S, Reinar WB, Grove H, Miller JR, Walenz BP, Knight J, Ekholm JM, Peluso P, Edvardsen RB, Tooming-Klunderud A, Skage M, Lien S, Jakobsen KS, Nederbragt AJ
The Atlantic salmon genome provides insights into rediploidization
Nature, May 12, 2016
Lien S … Walenz B … Davidson WS
Genomic insights into the Ixodes scapularis tick vector of Lyme disease
Nature communications, February 9, 2016
Gulia-Nuss M … Walenz BP, Koren S … Hill CA