Software articles within Nature Reviews Genetics

Featured

  • Tools of the Trade |

    In this Tools of the Trade article, Vipul Singhal and Nigel Chou describe BANKSY, a machine learning tool that harnesses gene expression gradients from the neighbourhood of a cell for cell typing and domain segmentation.

    • Vipul Singhal
    •  & Nigel Chou

  • Review Article |

    In this Review, Li and Durbin discuss how to generate telomere-to-telomere assemblies for large haploid or diploid genomes using currently available data types and algorithms, and outline remaining challenges in resolving highly repetitive sequences and polyploid genomes.

    • Heng Li
    •  & Richard Durbin

  • Review Article |

    In this Review, the authors summarize and discuss guidelines for omics benchmarking. They highlight common oversights and difficulties, offer guidance for frequently encountered issues and provide a structured form that can be used for comprehensive reporting of benchmarking studies.

    • Thomas G. Brooks
    • , Nicholas F. Lahens
    •  & Gregory R. Grant

  • Expert Recommendation |

    Practitioners in the field of single-cell omics are now faced with diverse options for analytical tools to process and integrate data from various molecular modalities. In an Expert Recommendation article, the authors provide guidance on robust single-cell data analysis, including choices of best-performing tools from benchmarking studies.

    • Lukas Heumos
    • , Anna C. Schaar
    •  & Fabian J. Theis

  • Review Article |

    In this Review, Berger and Yu discuss how the sheer amounts of sequence data create bottlenecks in downstream analytical pipelines that must be overcome by new analysis strategies, each with their own trade-offs for properties such as speed, accuracy and applicability.

    • Bonnie Berger
    •  & Yun William Yu

  • Review Article |

    In this Review the authors provide an overview of key algorithmic developments, popular tools and emerging technologies used in the bioinformatic analysis of genomes. They also describe how such analysis can identify point mutations, copy number alterations, structural variations and mutational signatures in cancer genomes.

    • Isidro Cortés-Ciriano
    • , Doga C. Gulhan
    •  & Peter J. Park

  • In Brief |

    In this paper in Nature Genetics, Atkinson et al. describe Tractor, a statistical framework and software package that enables admixed populations to be included in large-scale genomics studies.

    • Dorothy Clyde

  • Review Article |

    Computational tools to analyse RNA sequencing data often disregard or even misinterpret reads derived from transposable elements. This Review highlights the main challenges associated with the detection of transposable element expression, including mappability, sequence polymorphisms and transcript diversity, and discusses the experimental and computational strategies to overcome them.

    • Sophie Lanciano
    •  & Gael Cristofari

  • Review Article |

    In most human genes, RNA 3ʹ end cleavage and polyadenylation can occur at multiple, alternative sites, enabling the expression of distinct transcripts. Novel techniques to sequence RNA 3ʹ ends, coupled with innovative computational methods for studying the list of polyadenylation sites that they generate, have uncovered the roles of alternative cleavage and polyadenylation in both health and disease.

    • Andreas J. Gruber
    •  & Mihaela Zavolan

  • Analysis |

    Characterizing the essentiality of human genes provides insights into gene function and genome evolution and facilitates the clinical interpretation of genetic variants. This article analyses essentiality metrics based on the statistical intolerance to loss-of-function mutations in human population sequencing studies and discusses commonalities and distinctions relative to data sets from knockout mice and functional genomics screens in human cell culture. Implications for disease genetics and extrapolation to non-coding regions are also discussed.

    • István Bartha
    • , Julia di Iulio
    •  & Amalio Telenti

  • Review Article |

    Computer simulation of next-generation sequencing data can be extremely useful for assessing and validating biological models, benchmarking sequence analysis tools or gaining an understanding of specific data sets. Here, the authors review the functionality, requirements and applications of 23 currently available simulation tools and provide a guide for the selection of the most appropriate one.

    • Merly Escalona
    • , Sara Rocha
    •  & David Posada

  • Review Article |

    Forward genetic screens have a long history of uncovering the genetic mutations underlying phenotypes of interest. This Review describes how next-generation sequencing technology can be integrated into forward genetic screens not only to enhance their efficiency but also to allow them to be carried out using expanded repertoires of species, populations and experimental strategies.

    • Korbinian Schneeberger

  • Review Article |

    Systems biology is intrinsically reliant on software tools and data resources. Through looking at each stage in a systems biology workflow, this Review presents the available options and key challenges, and sets out the concept of an integrated software platform.

    • Samik Ghosh
    • , Yukiko Matsuoka
    •  & Hiroaki Kitano

Browse broader subjects

Browse Software across other nature.com journals