880 citations · 972 across the 9 of their papers we have counts for
9 papers
Distributed-Memory Parallel Contig Generation for De Novo Long-Read Genome Assembly
Giulia Guidi, Gabriel Raulet, Daniel Rokhsar +3
De novo genome assembly, i.e., rebuilding the sequence of an unknown genome from redundant and erroneous short sequences, is a key but computationally intensive step in many genomi…
Extreme-Scale De Novo Genome Assembly
Evangelos Georganas, Steven Hofmeyr, Rob Egan +4
De novo whole genome assembly reconstructs genomic sequence from short, overlapping, and potentially erroneous DNA segments and is one of the most important computations in modern…
Meraculous-2D: Haplotype-sensitive Assembly of Highly Heterozygous genomes
Eugene Goltsman, Isaac Ho, Daniel Rokhsar
While many short read assemblers attempt to simplify the de Brujin graph by identifying and resolving variant-induced bubbles to produce a haploid mosaic result, this approach is o…
Meraculous2: fast accurate short-read assembly of large polymorphic genomes
Jarrod A. Chapman, Isaac Y. Ho, Eugene Goltsman +1
We present Meraculous2, an update to the Meraculous short-read assembler that includes (1) handling of allelic variation using "bubble" structures within the de Bruijn graph, (2) i…
Chromosome-scale shotgun assembly using an in vitro method for long-range linkage
Nicholas H. Putnam, Brendan O'Connell, Jonathan C. Stites +7
Long-range and highly accurate de novo assembly from short-read data is one of the most pressing challenges in genomics. Recently, it has been shown that read pairs generated by pr…
How Much Phase Coherence Does a Pseudogap Need?
Paul E. Lammert, Daniel S. Rokhsar
It has been suggested that the ``pseudogap'' regime in cuprate superconductors, extending up to hudreds of degrees into the normal phase, reflects an incoherent d-wave pairing, wit…