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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Posted ContentDOI
Extensive transcriptional changes in the aphid species Myzus cerasi under different host environments associated with detoxification genes
Peter Thorpe,Carmen Escudero-Martinez,Carmen Escudero-Martinez,Sebastian Eves-van den Akker,Jorunn I. B. Bos,Jorunn I. B. Bos +5 more
TL;DR: In this article, the authors used Myzus cerasi (black cherry aphid) to assess aphid transcriptional differences between populations collected from primary hosts in the field and those adapted to secondary hosts under controlled environment conditions.
Journal ArticleDOI
Genome of Lindera glauca provides insights into the evolution of biosynthesis genes for aromatic compounds
Biao Xiong,Limei Zhang,Lu-Shan Xie,Linzhu Li,Xiangxiang He,Y.Z. Niu,Tianyuan Zhang,Shuai Liao,Shubin Dong,Zhi-Xiang Zhang +9 more
TL;DR: The chromosome-level genome assembly of Lindera glauca is described in this article , which contains 12 pseudochromosomes (2,092.2 Mb; scaffold N50: 186.5 Mb) and 65,145 protein-coding genes.
Journal ArticleDOI
Genome assembly of the roundjaw bonefish (Albula glossodonta), a vulnerable circumtropical sportfish
TL;DR: This paper assembled the genome of a roundjaw bonefish from Hawai'i, USA and evaluated population genetic connectivity between six atolls in the Western Indian Ocean with 38,355 SNP loci across 66 A. glossodonta individuals.
Journal ArticleDOI
Assessing and assuring interoperability of a genomics file format
TL;DR: A new verification system, Acidbio, is developed, which makes it easy to assess interoperability of software using the BED format, and therefore to identify areas for improvement in individual software packages.
Journal ArticleDOI
The reference genome of the Vernal Pool Tadpole Shrimp, Lepidurus packardi
Shannon Rose Kieran Blair,Joshua Hull,Merly Escalona,Amanda J. Finger,Shannon E. K. Joslin,Ruta Sahasrabudhe,Mohan P. A. Marimuthu,Oanh Nguyen,Noravit Chumchim,Emily Reister Morris,Samantha Velazquez,Andrea D. Schreier +11 more
TL;DR: This resource represents the first scaffold-level genome of any Lepidurus species and produced a predicted gene set for this species trained on the Daphnia magna set of genes and predicted 17,650 genes that can aid researchers in understanding the evolution and adaptive potential of alternative reproductive modes within this species.
References
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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.
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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.
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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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