Brian Walenz
Emeritus Software Engineer
gmail.com
Bri wrote his last (professional) bug in Summer 2024.
He developed software -- Celera Assembler -- Canu -- Verkko -- for assembling sequencing reads generated by a wide variety of sequencing technology -- Sanger via the ABI 3730/3730xl -- 454 Life Sciences' GS20, FLX and Titanium -- Solexa/Illumina paired-end/mate-pair (though these largely failed to work) -- Pacific Biosciences' RS, Sequel, and HiFi -- Oxford Nanopore.
He thanks -- David Levine -- Sorin Istrail -- Granger Sutton -- Jason Miller -- Adam Phillippy -- for their mentoring, management and trust.
He now spends his time puttering in his workshop, fixing obsolete electronics, and dreaming of building a 1960's-era supercomputer inspired by the CDC 6600.
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.
Merfin
Evaluate variant calls and its combination with k-mer multiplicity
Merqury
Evaluate genome assemblies with k-mers and more
SALSA
A tool to scaffold long read assemblies with Hi-C data
Publications