Publications by authors named "Luiz Irber"

Cyanobacteria form diverse communities and are important primary producers in Antarctic freshwater environments, but their geographic distribution patterns in Antarctica and globally are still unresolved. There are however few genomes of cultured cyanobacteria from Antarctica available and therefore metagenome-assembled genomes (MAGs) from Antarctic cyanobacteria microbial mats provide an opportunity to explore distribution of uncultured taxa. These MAGs also allow comparison with metagenomes of cyanobacteria enriched communities from a range of habitats, geographic locations, and climates.

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Article Synopsis
  • Evaluating metagenomic software is crucial for enhancing the interpretation of metagenomes, and the CAMI II challenge focused on this by using complex datasets from numerous genomes and plasmids.
  • The analysis of 5,002 results from 76 software versions showed significant advancements in assembly, especially with long-read data, although challenges remained with related strains and genome recovery.
  • Findings indicated that while taxon profilers improved, they struggled with viruses and Archaea, highlighting the need for better reproducibility in clinical pathogen detection and guiding researchers in method selection based on efficiency and performance metrics.
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Genomic surveillance can inform effective public health responses to pathogen outbreaks. However, integration of non-local data is rarely done. We investigate two large hospital outbreaks of a carbapenemase-carrying strain in Germany and show the value of contextual data.

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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 workflows that include multiple analytic tools and require incremental development as experimental insights demand tool and parameter modifications. These workflows can produce hundreds to thousands of intermediate files and results that must be integrated for biological insight.

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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. sourmash signatures can be used to estimate sequence similarity between very large data sets quickly and in low memory, and can be used to search large databases of genomes for matches to query genomes and metagenomes. sourmash is implemented in C++, Rust, and Python, and is freely available under the BSD license at http://github.

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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 haplotype phasing of mixtures of similar sequences. Here we demonstrate a method to reconstruct the sequences of individual nucleic acid molecules up to 11.

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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 data structure, a compressible De Bruijn graph representation, De Bruijn graph partitioning, and digital normalization. khmer is implemented in C++ and Python, and is freely available under the BSD license at  https://github.

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