Brian Walenz
Software Engineer (alum)
brian.walenz
nih.gov
nih.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
Verkko
Verkko is a hybrid genome assembly pipeline developed for telomere-to-telomere assembly of long accurate (e.g. PacBio HiFi) and ultra-long (e.g. Oxford Nanopore UL) reads. Verkko is Finnish for net, mesh and graph.
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
Publications