Journal ArticleDOI
GenomeTools: A Comprehensive Software Library for Efficient Processing of Structured Genome Annotations
TLDR
The GenomeTools, a convenient and efficient software library and associated software tools for developing bioinformatics software intended to create, process or convert annotation graphs, strictly follow the annotation graph approach, offering a unified graph-based representation.Abstract:
Genome annotations are often published as plain text files describing genomic features and their subcomponents by an implicit annotation graph. In this paper, we present the GenomeTools, a convenient and efficient software library and associated software tools for developing bioinformatics software intended to create, process or convert annotation graphs. The GenomeTools strictly follow the annotation graph approach, offering a unified graph-based representation. This gives the developer intuitive and immediate access to genomic features and tools for their manipulation. To process large annotation sets with low memory overhead, we have designed and implemented an efficient pull-based approach for sequential processing of annotations. This allows to handle even the largest annotation sets, such as a complete catalogue of human variations. Our object-oriented C-based software library enables a developer to conveniently implement their own functionality on annotation graphs and to integrate it into larger workflows, simultaneously accessing compressed sequence data if required. The careful C implementation of the GenomeTools does not only ensure a light-weight memory footprint while allowing full sequential as well as random access to the annotation graph, but also facilitates the creation of bindings to a variety of script programming languages (like Python and Ruby) sharing the same interface.read more
Citations
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Journal ArticleDOI
The digital biomarker discovery pipeline: An open-source software platform for the development of digital biomarkers using mHealth and wearables data.
Brinnae Bent,Ke Wang,Emilia Grzesiak,Chentian Jiang,Yuankai Qi,Yihang Jiang,Peter J. Cho,Kyle Zingler,Felix Ikponmwosa Ogbeide,Arthur Zhao,Ryan Runge,Ida Sim,Jessilyn Dunn +12 more
TL;DR: This work presents the first comprehensive, open-source software platform for end-to-end digital biomarker development: The Digital Biomarker Discovery Pipeline (DBDP), and details the general DBDP framework as well as three robust modules within the DBDP that have been developed for specificdigital biomarker discovery use cases.
Journal ArticleDOI
Genome compartmentalization predates species divergence in the plant pathogen genus Zymoseptoria
Alice Feurtey,Alice Feurtey,Cécile Lorrain,Cécile Lorrain,Cécile Lorrain,Daniel Croll,Christoph J. Eschenbrenner,Christoph J. Eschenbrenner,Michael Freitag,Michael Habig,Michael Habig,Janine Haueisen,Janine Haueisen,Mareike Möller,Mareike Möller,Mareike Möller,Klaas Schotanus,Klaas Schotanus,Klaas Schotanus,Eva H. Stukenbrock,Eva H. Stukenbrock +20 more
TL;DR: A high level of conservation in genomic, epigenomic and transcriptomic composition and structure across the genus Zymoseptoria is described, which allows the maintenance of a functional core genome co-occurring with a highly variable accessory genome.
Journal ArticleDOI
A new look at the LTR retrotransposon content of the chicken genome
TL;DR: This work suggests that there is no deficit of LTR retrotransposons within the Galliformes relative to other birds, or to mammalian genomes when scaled for the three-fold difference in genome size.
Journal ArticleDOI
Can we use it? On the utility of de novo and reference-based assembly of Nanopore data for plant plastome sequencing.
TL;DR: Nanopore long reads are a suitable alternative to Illumina short reads in plastome phylogenomics because few errors remain in the finalized assembly, which can be easily masked in phylogenetic analyses without loss in analytical accuracy.
Journal ArticleDOI
Northern Spotted Owl (Strix occidentalis caurina) Genome: Divergence with the Barred Owl (Strix varia) and Characterization of Light-Associated Genes.
Zachary R. Hanna,James B. Henderson,Jeffrey D. Wall,Christopher A. Emerling,Jérôme Fuchs,Jérôme Fuchs,Charles Runckel,Charles Runckel,David P. Mindell,Rauri C. K. Bowie,Joseph L. DeRisi,Joseph L. DeRisi,John P. Dumbacher +12 more
TL;DR: It is suggested that most light-associated gene functions have been maintained in owls and their loss has not proceeded to the same extent as in other dim-light-adapted vertebrates.
References
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BEDTools: a flexible suite of utilities for comparing genomic features
Aaron R. Quinlan,Ira M. Hall +1 more
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The variant call format and VCFtools
Petr Danecek,Adam Auton,Gonçalo R. Abecasis,Cornelis A. Albers,Eric Banks,Mark A. DePristo,Robert E. Handsaker,Gerton Lunter,Gabor T. Marth,Stephen T. Sherry,Gilean McVean,Richard Durbin +11 more
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