Luiz Irber
University of California, Davis
26 Papers
26 Citations
Luiz Irber is an academic researcher from University of California, Davis. The author has contributed to research in topics: Biology & Genome. The author has an hindex of 8, co-authored 19 publications. Previous affiliations of Luiz Irber include National Institute for Space Research & University of California.
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Papers
The khmer software package: enabling efficient nucleotide sequence analysis.
Michael R. Crusoe,Hussien F. Alameldin,Sherine Awad,Elmar Boucher,Adam Caldwell,Reed A. Cartwright,Amanda Charbonneau,Bede Constantinides,Greg Edvenson,Scott Fay,Jacob Fenton,Thomas Fenzl,Jordan A. Fish,Leonor Garcia-Gutierrez,Phillip Garland,Jonathan Gluck,Ivan Gonzalez,Sarah Guermond,Jiarong Guo,Aditi Gupta,Joshua R. Herr,Adina Howe,Alex Hyer,Andreas Härpfer,Luiz Irber,Rhys Kidd,David Lin,Justin Lippi,Tamer A. Mansour,Pamela McA'Nulty,Eric McDonald,Jessica E. Mizzi,Kevin D Murray,Joshua R. Nahum,Kaben G. Nanlohy,Alexander J. Nederbragt,Humberto Ortiz-Zuazaga,Jeramia Ory,Jason Pell,Charles Pepe-Ranney,Zachary N. Russ,Erich M. Schwarz,Camille Scott,Josiah Seaman,Scott Sievert,Jared T. Simpson,Connor T. Skennerton,James S. Spencer,Ramakrishnan Srinivasan,Daniel S. Standage,James A. Stapleton,Susan R. Steinman,Joe Stein,Benjamin R Taylor,Will Trimble,Heather L. Wiencko,Michael Wright,Brian Wyss,Qingpeng Zhang,en zyme,C. Titus Brown +60 more
TL;DR: Khmer as discussed by the authors is a free software library for working efficiently with fixed length DNA words, or k-mers, which provides implementations of a probabilistic k-mer counting data structure, a compressible De Bruijn graph representation, De Bruhen graph partitioning, and digital normalization.
sourmash: a library for MinHash sketching of DNA
C. Titus Brown,Luiz Irber +1 more
TL;DR: Sourmash is a toolbox for creating, comparing, and manipulating MinHash sketches of genomic data that provide a lightweight way to store “signatures” of large DNA or RNA sequence collections, and then compare or search them using a Jaccard index.
Large-scale sequence comparisons with sourmash.
TL;DR: The sourmash software package uses MinHash-based sketching to create “signatures”, compressed representations of DNA, RNA, and protein sequences, that can be stored, searched, explored, and taxonomically annotated.
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Lightweight compositional analysis of metagenomes with FracMinHash and minimum metagenome covers
Luiz Irber,Phillip T. Brooks,Taylor Reiter,N. T. Pierce-Ward,Mahmudur Rahman Hera,David Koslicki,C. Titus Brown +6 more
TL;DR: The FracMinHash sketching technique is investigated, a derivative of modulo hash that supports Jaccard containment estimation between sets of different sizes, and the minimum metagenome cover can be used to guide the selection of reference genomes for read mapping.
Haplotype-Phased Synthetic Long Reads from Short-Read Sequencing.
James A. Stapleton,Jeongwoon Kim,John P. Hamilton,Ming Wu,Luiz Irber,Rohan Maddamsetti,Bryan Briney,Bryan Briney,Linsey Newton,Dennis R. Burton,Dennis R. Burton,C. Titus Brown,C. Titus Brown,Christina Chan,C. Robin Buell,Timothy A. Whitehead +15 more
TL;DR: This work demonstrates a method to reconstruct the sequences of individual nucleic acid molecules up to 11.6 kilobases in length from short (150-bp) reads, which generates sequencing libraries in three days from less than one microgram of DNA in a single-tube format without custom equipment or specialized expertise.