Brian Walenz

Software Engineer

brian.walenznih.gov

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.

Software

Merqury

Evaluate genome assemblies with k-mers and more

SALSA

A tool to scaffold long read assemblies with Hi-C data

Canu

A single molecule sequence assembler for genomes large and small

Celera Assembler PBcR

PacBio read correction and assembly pipeline [ retired ]
Publications
The genomic structure of a human chromosome 22 nucleolar organizer region determined by TAR cloning
Scientific reports, February 4, 2021
Kim JH, Noskov VN, Ogurtsov AY, Nagaraja R, Petrov N, Liskovykh M, Walenz BP, Lee HS, Kouprina N, Phillippy AM, Shabalina SA, Schlessinger D, Larionov V