Fast and robust metagenomic sequence comparison through sparse chaining with skani

Article Biochemical Research Methods

The minimizer Jaccard estimator is biased and inconsistent

Mahdi Belbasi et al.

Summary: This article investigates the bias and inconsistency issues of the minimizer sketch in estimating Jaccard similarity, and its impact on data processing accuracy.

BIOINFORMATICS (2022)

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Article Multidisciplinary Sciences

The OceanDNA MAG catalog contains over 50,000 prokaryotic genomes originated from various marine environments

Yosuke Nishimura et al.

Summary: The genomic repertoire of marine microorganisms is expanded through the collection and reconstruction of a large number of marine metagenomes, leading to the discovery of novel microbial lineages and a significant increase in known phylogenetic diversity.

SCIENTIFIC DATA (2022)

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Article Multidisciplinary Sciences

A compendium of 32,277 metagenome-assembled genomes and over 80 million genes from the early-life human gut microbiome

Shuqin Zeng et al.

Summary: The authors present a large-scale resource of the early-life human gut microbiome, including transcriptomes and proteomes, from children under three years old. This resource provides detailed information on the development and disturbances of the gut microbiome in early life.

NATURE COMMUNICATIONS (2022)

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Article Biochemical Research Methods

Theory of local k-mer selection with applications to long-read alignment

Jim Shaw et al.

Summary: This study investigates the conservation metric for k-mer selection methods, deriving exact expressions for various methods and demonstrating an increase in mapped reads using a more conserved k-mer selection method. However, the trade-off includes the potential for increased runtime due to the repetitive nature of the selected k-mers. The findings provide insights on using new k-mer selection methods to optimize for speed and alignment quality.

BIOINFORMATICS (2022)

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Article Biochemical Research Methods

The Statistics of k-mers from a Sequence Undergoing a Simple Mutation Process Without Spurious Matches

Antonio Blanca et al.

Summary: In this study, we investigate the impact of a simple mutation process on k-mers in sequences such as genomes or reads. We derive the expected values and variances of mutated k-mers, as well as islands and oceans, and provide hypothesis tests and confidence intervals based on the observed number of mutated k-mers or Jaccard similarity.

JOURNAL OF COMPUTATIONAL BIOLOGY (2022)

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Article Biotechnology & Applied Microbiology

A genomic catalog of Earth's microbiomes

Stephen Nayfach et al.

Summary: Reconstructing bacterial and archaeal genomes from shotgun metagenomes has led to the creation of a comprehensive catalog representing a significant expansion of the known phylogenetic diversity of bacteria and archaea. This resource is available for streamlined comparative analyses, interactive exploration, metabolic modeling, and bulk download, demonstrating the utility of genome-centric approaches for understanding genomic properties of uncultivated microorganisms.

NATURE BIOTECHNOLOGY (2021)

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Article Microbiology