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
A high-quality genome assembly and annotation of the dark-eyed junco <i>Junco hyemalis</i>, a recently diversified songbird
TL;DR: The dark-eyed junco (Junco hyemalis) is one of the most common passerines of North America, and has served as a model organism in studies related to ecophysiology, behavior, and evolutionary biology for over a century as mentioned in this paper .
Journal ArticleDOI
TextFormats: Simplifying the definition and parsing of text formats in bioinformatics
TL;DR: This manuscript presents the open source software library and toolset TextFormats, which aims at simplifying the definition and parsing of text formats, and the specifications of several common existing bioinformatics formats are included.
Posted ContentDOI
The haplotype-resolved chromosome pairs and transcriptome of a heterozygous diploid African cassava cultivar
Weihong Qi,Y.-W. Lim,Andrea Patrignani,P. Schlaepfer,Anna Bratus-Neuenschwander,S. Grueter,C. Chanez,Nathalie Rodde,Elisa Prat,Sonia Vautrin,M.-A. Fustier,Diogo Pratas,Diogo Pratas,Ralph Schlapbach,Wilhelm Gruissem +14 more
TL;DR: In this paper, a haplotype-resolved transcriptome of cassava was used to build a pan-genome of the diploid African cassava variety TME204.
Journal ArticleDOI
Evolution of woody plants to the land‐sea interface – The atypical genomic features of mangroves with atypical phenotypic adaptation
TL;DR: It is concluded that the mangroves with atypical phenotypes also haveAtypical genomic evolution.
Book ChapterDOI
Integrated Genome-Scale Analysis and Northern Blot Detection of Retrotransposon siRNAs Across Plant Species.
Marcel Böhrer,Bart Rymen,Christophe Himber,Aude Gerbaud,David Pflieger,Debbie Laudencia-Chingcuanco,Amy Cartwright,John P. Vogel,Richard Sibout,Todd Blevins +9 more
TL;DR: The integration of de novo TE annotation, small RNA-seq profiling, and northern blotting, as outlined here, will facilitate the comparative genomic analysis of RNA silencing in crop plants and non-model species.
References
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Book
Design Patterns: Elements of Reusable Object-Oriented Software
TL;DR: The book is an introduction to the idea of design patterns in software engineering, and a catalog of twenty-three common patterns, which most experienced OOP designers will find out they've known about patterns all along.
Book
Introduction to Algorithms
TL;DR: The updated new edition of the classic Introduction to Algorithms is intended primarily for use in undergraduate or graduate courses in algorithms or data structures and presents a rich variety of algorithms and covers them in considerable depth while making their design and analysis accessible to all levels of readers.
Journal ArticleDOI
BEDTools: a flexible suite of utilities for comparing genomic features
Aaron R. Quinlan,Ira M. Hall +1 more
TL;DR: A new software suite for the comparison, manipulation and annotation of genomic features in Browser Extensible Data (BED) and General Feature Format (GFF) format, which allows the user to compare large datasets (e.g. next-generation sequencing data) with both public and custom genome annotation tracks.
Journal ArticleDOI
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
TL;DR: VCFtools is a software suite that implements various utilities for processing VCF files, including validation, merging, comparing and also provides a general Perl API.
Book ChapterDOI
Introduction to Algorithms
TL;DR: This chapter provides an overview of the fundamentals of algorithms and their links to self-organization, exploration, and exploitation.
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