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 genome and lifestage-specific transcriptomes of a plant-parasitic nematode and its host reveal susceptibility genes involved in trans-kingdom synthesis of vitamin B5
TL;DR: In this article , the authors used a combination of bioinformatic, genetic, and biochemical approaches to identify susceptibility genes for plant-parasitic nematode susceptibility genes, and showed that congruent differential expression of metabolic pathways in the infection hologenome represents a new way to find susceptibility genes.
Journal ArticleDOI
Draft Genome Assembly of the Freshwater Apex Predator Wels Catfish (Silurus glanis) Using Linked-Read Sequencing.
Mikhail Ozerov,Mikhail Ozerov,Martin Flajšhans,Kristina Noreikiene,Anti Vasemägi,Anti Vasemägi,Riho Gross +6 more
TL;DR: A de novo assembly and annotation of the whole genome sequence of a female S. glanis and the highly continuous genome assembly will be an invaluable resource for aquaculture genomics, genetics, conservation, and breeding research of S.glanis.
Journal ArticleDOI
Explore, edit and leverage genomic annotations using Python GTF toolkit.
Frédéric Lopez,Guillaume Charbonnier,Yasmina Kermezli,Mohamed Belhocine,Quentin Ferré,N. Zweig,Mourad Aribi,Aitor González,Salvatore Spicuglia,Denis Puthier +9 more
TL;DR: The pygtftk package greatly simplifies the annotation of GTF files with external information while providing advance tools to perform gene analyses.
Journal ArticleDOI
The Untapped Australasian Diversity of Astaxanthin-Producing Yeasts with Biotechnological Potential-Phaffia australis sp. nov. and Phaffia tasmanica sp. nov.
Márcia David-Palma,Diego Libkind,Patrícia H. Brito,Margarida Silva,Nicolás Bellora,Marco A. Coelho,Marco A. Coelho,Joseph Heitman,Paula Gonçalves,José Paulo Sampaio +9 more
TL;DR: The genomes of two Australasian lineages that are markedly distinct from P. rhodozyma are analyzed and support the recognition of two novel Phaffia species, for which the names of P. australis sp.
Journal ArticleDOI
Role of Dicer-Dependent RNA Interference in Regulating Mycoparasitic Interactions.
Edoardo Piombo,Ramesh R. Vetukuri,Anders Broberg,Pruthvi B. Kalyandurg,Sandeep K. Kushwaha,Dan Funck Jensen,Magnus Karlsson,Mukesh Dubey +7 more
TL;DR: In this article, the role of DCL-dependent RNA interference in mycoparasitic interactions between C. rosea and B. cinerea and Fusarium graminearum was investigated.
References
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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.
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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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