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

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
Effect of Sequence Depth and Length in Long-read Assembly of the Maize Inbred NC358
Nature Communications, May 8, 2020
Ou S, Liu J, Chougule KM, Fungtammasan A, Seetharam A, Stein J, Llaca V, Manchanda N, Gilbert AM, Wei X, Chin C, Hufnagel DE, Pedersen S, Snodgrass S, Fengler K, Woodhouse M, Walenz BP, Koren S, Phillippy AM, Hannigan B, Kelly DR, Hirsch CN, Hufford MB, Ware D