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Published year: 20162
Colib’read on galaxy: a tools suite dedicated to biological information extraction from raw NGS reads

Abstract (Expand)

With next-generation sequencing (NGS) technologies, the life sciences face a deluge of raw data. Classical analysis processes for such data often begin with an assembly step, needing large amounts of … computing resources, and potentially removing or modifying parts of the biological information contained in the data. Our approach proposes to focus directly on biological questions, by considering raw unassembled NGS data, through a suite of six command-line tools. Dedicated to ‘whole-genome assembly-free’ treatments, the Colib’read tools suite uses optimized algorithms for various analyses of NGS datasets, such as variant calling or read set comparisons. Based on the use of a de Bruijn graph and bloom filter, such analyses can be performed in a few hours, using small amounts of memory. Applications using real data demonstrate the good accuracy of these tools compared to classical approaches. To facilitate data analysis and tools dissemination, we developed Galaxy tools and tool shed repositories. With the Colib’read Galaxy tools suite, we enable a broad range of life scientists to analyze raw NGS data. More importantly, our approach allows the maximum biological information to be retained in the data, and uses a very low memory footprint.

Authors: Yvan Le Bras, Olivier Collin, Cyril Monjeaud, Vincent Lacroix, Éric Rivals, Claire Lemaitre, Vincent Miele, Gustavo Sacomoto, Camille Marchet, Bastien Cazaux, Amal Zine El Aabidine, Leena Salmela, Susete Alves-Carvalho, Alexan Andrieux, Raluca Uricaru, Pierre Peterlongo

Date Published: 1st Dec 2016

Publication Type: Not specified

Genetic basis of nitrogen use efficiency and yield stability across environments in winter rapeseed.

Abstract (Expand)

Nitrogen use efficiency is an important breeding trait that can be modified to improve the sustainability of many crop species used in agriculture. Rapeseed is a major oil crop with low nitrogen use … efficiency, making its production highly dependent on nitrogen input. This complex trait is suspected to be sensitive to genotype × environment interactions, especially genotype × nitrogen interactions. Therefore, phenotyping diverse rapeseed populations under a dense network of trials is a powerful approach to study nitrogen use efficiency in this crop. The present study aimed to determine the quantitative trait loci (QTL) associated with yield in winter oilseed rape and to assess the stability of these regions under contrasting nitrogen conditions for the purpose of increasing nitrogen use efficiency.

Authors: Anne-Sophie Bouchet, Anne Laperche, Christine Bissuel-Belaygue, Cécile Baron, Jérôme Morice, Mathieu Rousseau-Gueutin, Jean-Eric Dheu, Pierre George, Xavier Pinochet, Thomas Foubert, Olivier Maes, Damien Dugué, Florent Guinot, Nathalie Nesi

Date Published: 16th Sep 2016

Publication Type: Not specified

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