User profiles for Luiz C. Irber
 | Luiz IrberStaff Bioinformatics Engineer, Ancestry Verified email at ucdavis.edu Cited by 1229 |
[HTML][HTML] Haplotype-phased synthetic long reads from short-read sequencing
Next-generation DNA sequencing has revolutionized the study of biology. However, the short
read lengths of the dominant instruments complicate assembly of complex genomes and …
read lengths of the dominant instruments complicate assembly of complex genomes and …
[HTML][HTML] Efficient cardinality estimation for k-mers in large DNA sequencing data sets: k-mer cardinality estimation
LC Irber Jr, CT Brown - biorxiv, 2016 - biorxiv.org
We present an open implementation of the HyperLogLog cardinality estimation sketch for
counting fixed-length substrings of DNA strings (“k-mers”). The HyperLogLog sketch …
counting fixed-length substrings of DNA strings (“k-mers”). The HyperLogLog sketch …
[BOOK][B] Decentralizing indices for genomic data
LC Irber Jr - 2020 - search.proquest.com
Biology as a field is being transformed by the increasing availability of data, especially
genomic sequencing data. Computational methods that can adapt and take advantage of this …
genomic sequencing data. Computational methods that can adapt and take advantage of this …
[HTML][HTML] The khmer software package: enabling efficient nucleotide sequence analysis
The khmer package is a freely available software library for working efficiently with fixed length
DNA words, or k-mers. khmer provides implementations of a probabilistic k-mer counting …
DNA words, or k-mers. khmer provides implementations of a probabilistic k-mer counting …
[HTML][HTML] Critical assessment of metagenome interpretation: the second round of challenges
Evaluating metagenomic software is key for optimizing metagenome interpretation and focus
of the Initiative for the Critical Assessment of Metagenome Interpretation (CAMI). The CAMI …
of the Initiative for the Critical Assessment of Metagenome Interpretation (CAMI). The CAMI …
sourmash: a library for MinHash sketching of DNA
MinHash sketches provide a lightweight way to store “signatures” of large DNA or RNA
sequence collections, and then compare or search them using a Jaccard index. MinHash …
sequence collections, and then compare or search them using a Jaccard index. MinHash …
[HTML][HTML] Large-scale sequence comparisons with sourmash
The sourmash software package uses MinHash-based sketching to create “signatures”,
compressed representations of DNA, RNA, and protein sequences, that can be stored, searched…
compressed representations of DNA, RNA, and protein sequences, that can be stored, searched…
Lightweight compositional analysis of metagenomes with FracMinHash and minimum metagenome covers
The identification of reference genomes and taxonomic labels from metagenome data underlies
many microbiome studies. Here we describe two algorithms for compositional analysis …
many microbiome studies. Here we describe two algorithms for compositional analysis …
[HTML][HTML] Climate simulation and change in the Brazilian climate model
…, SN Figueroa, MC Costa, M Baptista, L Irber… - Journal of …, 2013 - journals.ametsoc.org
… c. Model climatology and systematic errors … Doutriaux, C., and KE Tayler, cited 2011:
Climate Model Output Rewriter (CMOR). CMOR 2.0 Users Guide. [Available online at http://www2-pcmdi.llnl.gov/cmor/documentation/cmor-2-0-users-guide-html.] …
Climate Model Output Rewriter (CMOR). CMOR 2.0 Users Guide. [Available online at http://www2-pcmdi.llnl.gov/cmor/documentation/cmor-2-0-users-guide-html.] …
Streamlining data-intensive biology with workflow systems
As the scale of biological data generation has increased, the bottleneck of research has
shifted from data generation to analysis. Researchers commonly need to build computational …
shifted from data generation to analysis. Researchers commonly need to build computational …