Cnidaria: fast, reference-free clustering of raw and assembled genome and transcriptome NGS data

Background: Identification of biological specimens is a major requirement for a range of applications. Reference-free methods analyse unprocessed sequencing data without relying on prior knowledge, but generally do not scale to arbitrarily large genomes and arbitrarily large phylogenetic distances. Results: We present Cnidaria, a practical tool for clustering genomic and transcriptomic data with no limitation on genome size or phylogenetic distances. We successfully simultaneously clustered 169 genomic and transcriptomic datasets from 4 kingdoms, achieving 100% identification accuracy at supra-species level and 78% accuracy for species level. Discussion: CNIDARIA allows for fast, resource-efficient comparison and identification of both raw and assembled genome and transcriptome data. This can help answer both fundamental (e.g. in phylogeny, ecological diversity analysis) and practical questions (e.g. sequencing quality control, primer design).Comment: 47 pages, 13 figure

BioContainers: An open-source and community-driven framework for software standardization

Motivation BioContainers (biocontainers.pro) is an open-source and community-driven framework which provides platform independent executable environments for bioinformatics software. BioContainers allows labs of all sizes to easily install bioinformatics software, maintain multiple versions of the same software and combine tools into powerful analysis pipelines. BioContainers is based on popular open-source projects Docker and rkt frameworks, that allow software to be installed and executed under an isolated and controlled environment. Also, it provides infrastructure and basic guidelines to create, manage and distribute bioinformatics containers with a special focus on omics technologies. These containers can be integrated into more comprehensive bioinformatics pipelines and different architectures (local desktop, cloud environments or HPC clusters). Availability and Implementation The software is freely available at github.com/BioContainers/.publishedVersio

BioContainers: An open-source and community-driven framework for software standardization

Motivation BioContainers (biocontainers.pro) is an open-source and community-driven framework which provides platform independent executable environments for bioinformatics software. BioContainers allows labs of all sizes to easily install bioinformatics software, maintain multiple versions of the same software and combine tools into powerful analysis pipelines. BioContainers is based on popular open-source projects Docker and rkt frameworks, that allow software to be installed and executed under an isolated and controlled environment. Also, it provides infrastructure and basic guidelines to create, manage and distribute bioinformatics containers with a special focus on omics technologies. These containers can be integrated into more comprehensive bioinformatics pipelines and different architectures (local desktop, cloud environments or HPC clusters). Availability and Implementation The software is freely available at github.com/BioContainers/

The genome of the stress-tolerant wild tomato species Solanum pennellii

Solanum pennellii is a wild tomato species endemic to Andean regions in South America, where it has evolved to thrive in arid habitats. Because of its extreme stress tolerance and unusual morphology, it is an important donor of germplasm for the cultivated tomato Solanum lycopersicum1. Introgression lines (ILs) in which large genomic regions of S. lycopersicum are replaced with the corresponding segments from S. pennellii can show remarkably superior agronomic performance2. Here we describe a high-quality genome assembly of the parents of the IL population. By anchoring the S. pennellii genome to the genetic map, we define candidate genes for stress tolerance and provide evidence that transposable elements had a role in the evolution of these traits. Our work paves a path toward further tomato improvement and for deciphering the mechanisms underlying the myriad other agronomic traits that can be improved with S. pennellii germplasm.Fil: Bolger, Anthony. Aachen University; Alemania. Institut Max Planck fur Molekulare Physiologie; AlemaniaFil: Scossa, Federico. Institut Max Planck fur Molekulare Physiologie; Alemania. Consiglio per la Ricerca in Agricoltura e l'Analisi del l'Economía Agraria; ItaliaFil: Bolger, Marie E.. Institut Max Planck fur Molekulare Physiologie; Alemania. Forschungszentrum Jülich; AlemaniaFil: Lanz, Christa. Institut Max Planck fur Molekulare Physiologie; AlemaniaFil: Maumus, Florian. Institut National de la Recherche Agronomique; FranciaFil: Tohge, Takayuki. Institut Max Planck fur Molekulare Physiologie; AlemaniaFil: Quesneville, Hadi. Institut National de la Recherche Agronomique; FranciaFil: Alseekh, Saleh. Institut Max Planck fur Molekulare Physiologie; AlemaniaFil: Sørensen, Iben. Cornell University; Estados UnidosFil: Lichtenstein, Gabriela. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Instituto Nacional de Tecnología Agropecuaria. Centro de Investigación en Ciencias Veterinarias y Agronómicas. Instituto de Biotecnología; ArgentinaFil: Fich, Eric A.. Cornell University; Estados UnidosFil: Conte, Mariana. Instituto Nacional de Tecnología Agropecuaria. Centro de Investigación en Ciencias Veterinarias y Agronómicas; ArgentinaFil: Keller, Heike. Institut Max Planck fur Molekulare Physiologie; AlemaniaFil: Schneeberger, Korbinian. Institut Max Planck fur Molekulare Physiologie; Alemania. Max Planck Institute for Plant Breeding Research; AlemaniaFil: Schwacke, Rainer. Institut Max Planck fur Molekulare Physiologie; Alemania. Forschungszentrum Jülich; AlemaniaFil: Ofner, Itai. The Hebrew University of Jerusalem; IsraelFil: Vrebalov, Julia. Cornell University; Estados UnidosFil: Xu, Yimin. Cornell University; Estados UnidosFil: Osorio, Sonia. Institut Max Planck fur Molekulare Physiologie; Alemania. Universidad de Málaga; EspañaFil: Aflitos, Saulo Alves. University of Agriculture Wageningen; Países BajosFil: Schijlen, Elio. University of Agriculture Wageningen; Países BajosFil: Jiménez Goméz, José M.. Max Planck Institute for Plant Breeding Research; Alemania. Institut National de la Recherche Agronomique; FranciaFil: Ryngajllo, Malgorzata. Institut Max Planck fur Molekulare Physiologie; AlemaniaFil: Kimura, Seisuke. University of California at Davis; Estados UnidosFil: Kumar, Ravi. University of California at Davis; Estados UnidosFil: Koenig, Daniel. Institut Max Planck fur Molekulare Physiologie; Alemania. University of California at Davis; Estados UnidosFil: Headland, Lauren R.. University of California at Davis; Estados UnidosFil: Maloof, Julin N.. University of California at Davis; Estados UnidosFil: Sinha, Neelima. University of California at Davis; Estados UnidosFil: Van Ham, Roeland C. H. J.. University of Agriculture Wageningen; Países Bajo

The genome of the stress-tolerant wild tomato species Solanum pennellii.

Solanum pennellii is a wild tomato species endemic to Andean regions in South America, where it has evolved to thrive in arid habitats. Because of its extreme stress tolerance and unusual morphology, it is an important donor of germplasm for the cultivated tomato Solanum lycopersicum. Introgression lines (ILs) in which large genomic regions of S. lycopersicum are replaced with the corresponding segments from S. pennellii can show remarkably superior agronomic performance. Here we describe a high-quality genome assembly of the parents of the IL population. By anchoring the S. pennellii genome to the genetic map, we define candidate genes for stress tolerance and provide evidence that transposable elements had a role in the evolution of these traits. Our work paves a path toward further tomato improvement and for deciphering the mechanisms underlying the myriad other agronomic traits that can be improved with S. pennellii germplasm

The genome of the stress-tolerant wild tomato species Solanum pennellii

Solanum pennellii is a wild tomato species endemic to Andean regions in South America, where it has evolved to thrive in arid habitats. Because of its extreme stress tolerance and unusual morphology, it is an important donor of germplasm for the cultivated tomato Solanum lycopersicum. Introgression lines (ILs) in which large genomic regions of S. lycopersicum are replaced with the corresponding segments from S. pennellii can show remarkably superior agronomic performance. Here we describe a high-quality genome assembly of the parents of the IL population. By anchoring the S. pennellii genome to the genetic map, we define candidate genes for stress tolerance and provide evidence that transposable elements had a role in the evolution of these traits. Our work paves a path toward further tomato improvement and for deciphering the mechanisms underlying the myriad other agronomic traits that can be improved with S. pennellii germplasm