9,322 Works

Malus baccata cultivar:Shandingzi Genome sequencing and assembly

Sequencing of a wild apple (Malus baccata) genome to unravels the difference between cultivated and wild apples

Sorghum bicolor Genome sequencing

Resequencing of sorghum species.

Peer review of \"GADMA: Genetic algorithm for inferring demographic history of multiple populations from allele frequency spectrum data\"

Ryan Gutenkunst
This is the open peer reviewers comments and recommendations regarding the submitted GigaScience article and/or dataset.

Supporting data for \"Binning unassembled short reads based on k-mer covariance using sparse coding\"

, , , & Brüls Thomas
Sequence binning techniques enable the recovery of a growing number of genomes from complex microbial metagenomes and typically require prior metagenome assembly, incurring the computational cost and drawbacks of the latter, e.g. biases against low-abundance genomes and inability to conveniently assemble multi-terabyte datasets.
We present here a scalable pre-assembly binning scheme (i.e. operating on unassembled short reads) enabling latent genomes recovery by leveraging sparse dictionary learning and elastic-net regularization, and its use to recover hundreds of...

Supporting data for \"The Gene-Rich Genome of the Scallop Pecten maximus\"

Kenny J Nathan, McCarthy Shane, Dudchenko Olga, James Katherine, , , Dolucan Jale, Mead Dan, Oliver Karen, Omer Arina, Pelan Sarah, Ryan Yan, , , , Torrance James, Weisz David, Wipat Anil, Aiden Lieberman Erez, Howe Kerstin & Williams T Suzanne
The King Scallop, Pecten maximus, is distributed in shallow waters along the Atlantic coast of Europe. It forms the basis of a valuable commercial fishery and its ubiquity means that it plays a key role in coastal ecosystems and food webs. Like other filter feeding bivalves it can accumulate potent phytotoxins, to which it has evolved some immunity. The molecular origins of this immunity are of interest to evolutionary biologists, pharmaceutical companies and fisheries management....

Chromosome-level reference genome of the jellyfish Rhopilema esculentum

Li Yunfeng, Gao Lei, Pan Yongjia, Tian Meilin, Li Yulong, He Chongbo, Dong Ying, Sun Yamin & Zhou Zunchun
Jellyfish belong to the phylum Cnidaria, which occupies an important phylogenetic location in the early-branching Metazoa lineages. The jellyfish Rhopilema esculentum is an important fishery resource in China. However, the genome resource of R. esculentum has not been reported to date.
In this study, we constructed a chromosome-level genome assembly of R. esculentum using Pacific Biosciences, Illumina and Hi-C sequencing technologies. The final genome assembly was approximately 275.42 Mb, with a contig N50 length of 1.13...

Supporting data for \"CSA: A high-throughput chromosome-scale assembly pipeline for vertebrate genomes\"

Kuhl Heiner, Li Ling, , , Liang Xu-Fang &
Easy-to-use and fast bioinformatics pipelines for long-read assembly that go beyond the contig-level to generate high-quality chromosome-scale genomes from raw data remain scarce.
Chromosome Scale Assembler (CSA) is a novel computationally highly efficient bioinformatics pipeline that fills this gap. CSA integrates information from scaffolded assemblies (e.g. Hi-C or 10X Genomics) or even from diverged reference genomes into the assembly process. As CSA performs automated assembly of chromosome-sized scaffolds, we benchmark its performance against state-of-the art reference...

Supporting data for \"MaRe: Processing Big Data with Application Containers on Apache Spark\"

Capuccini Marco, Dahlö Martin, Toor Salman & Spjuth Ola
Life science is increasingly driven by Big Data analytics, and the MapReduce programming model has been proven successful for data-intensive analyses. However, current MapReduce frameworks offer poor support for reusing existing processing tools in bioinformatics pipelines. Further, these frameworks do not have native support for application containers, which are becoming popular in scientific data processing. Here we present MaRe, an open-source programming library which introduces support for Docker containers in Apache Spark. Apache Spark and...

Peer review of \"Chromosome-level genome assembly and annotation of the loquat (Eriobotrya japonica) genome\"

Robert Van Buren
This is the open peer reviewers comments and recommendations regarding the submitted GigaScience article and/or dataset.

Peer review of \"Interpretable and accurate prediction models for metagenomics data\"

Bonnie Hurwit
This is the open peer reviewers comments and recommendations regarding the submitted GigaScience article and/or dataset.

Peer review of \"An image dataset related to automated macrophage detection in immunostained lymphoma tissue samples\"

Guy M Hagen
This is the open peer reviewers comments and recommendations regarding the submitted GigaScience article and/or dataset.

Peer review of \"*-DCC: A platform to collect, annotate, and explore a large variety of sequencing experiments\"

Christophe Trefois
This is the open peer reviewers comments and recommendations regarding the submitted GigaScience article and/or dataset.

Peer review of \"*-DCC: A platform to collect, annotate, and explore a large variety of sequencing experiments\"

Adam Frankishl
This is the open peer reviewers comments and recommendations regarding the submitted GigaScience article and/or dataset.

Peer review of \"Chromosome-level genome assembly of Aldrichina grahami, a forensically important blowfly\"

Aaron Taron
This is the open peer reviewers comments and recommendations regarding the submitted GigaScience article and/or dataset.

Peer review of \"Chromosome-level genome assembly of Aldrichina grahami, a forensically important blowfly\"

Aaron Tarone
This is the open peer reviewers comments and recommendations regarding the submitted GigaScience article and/or dataset.

Peer review of \"Multi-omics Visualization Platform: An extensible Galaxy plug-in for multi-omics data visualization and exploration\"

Anil Thanki
This is the open peer reviewers comments and recommendations regarding the submitted GigaScience article and/or dataset.

Supporting data for \"Sequencing smart: De novo sequencing and assembly approaches for a non-model mammal.\"

Etherington John Graham, Heavens Darren, , Lister Ashleigh, , Garcia Gonzalo, Clavijo Bernardo, Macaulay Iain, Haerty Wilfried & Di Palma Federica
Whilst much sequencing effort has focused on key mammalian model organisms such as mouse and human, little is known about the correlation between genome sequencing techniques for non-model mammals and genome assembly quality. This is especially relevant to non-model mammals, where the samples to be sequenced are often degraded and low quality. A key aspect when planning a genome project is the choice of sequencing data to generate. This decision is driven by several factors,...

Peer review of \"Genome sequence of the agarwood tree Aquilaria sinensis (Lour.) Spreng: the first chromosome-level draft genome in the Thymelaeceae family\"

Caroline Belser
This is the open peer reviewers comments and recommendations regarding the submitted GigaScience article and/or dataset.

Peer review of \"Genome sequence of the agarwood tree Aquilaria sinensis (Lour.) Spreng: the first chromosome-level draft genome in the Thymelaeceae family\"

Fernando Cruz
This is the open peer reviewers comments and recommendations regarding the submitted GigaScience article and/or dataset.

Peer review of \"Comparative proteomics analysis of Tibetan hull-less barley under osmotic stress via data-independent acquisition mass spectrometry\"

This is the open peer reviewers comments and recommendations regarding the submitted GigaScience article and/or dataset.

Peer review of \"DeepPod: a convolutional neural network based quantification of fruit number in Arabidopsis\"

This is the open peer reviewers comments and recommendations regarding the submitted GigaScience article and/or dataset.

Peer review of \"Light-responsive expression atlas reveals the effects of light quality and intensity in Kalanchoë fedtschenkoi, a plant with crassulacean acid metabolism\"

Aureliano Bombarely
This is the open peer reviewers comments and recommendations regarding the submitted GigaScience article and/or dataset.

Supporting data for \"An improved pig reference genome sequence to enable pig genetics and genomics research\"

Warr Amanda, , Aken Bronwen, Beiki Hamid, Bickhart M Derek, Billis Konstantinos, Chow William, Eory Lel, , Flicek Paul, Girón G Carlos, Griffin K Darren, Hall Richard, , Hourlier Thibaut, Howe Kerstin, Hume David, Izuogu Osagie, Kim Kristi, Koren Sergey, Liu Haibou, , Martin J Fergal, Nonneman J Dan, O'Connor E Rebecca … & Archibald Alan
The domestic pig (Sus scrofa) is important both as a food source and as a biomedical model given its similarity in size, anatomy, physiology, metabolism, pathology and pharmacology to humans. The draft reference genome (Sscrofa10.2) of a purebred Duroc female pig established using older clone-based sequencing methods was incomplete and unresolved redundancies, short range order and orientation errors and associated misassembled genes limited its utility. We present two annotated highly contiguous chromosome-level genome assemblies created...

Peer review of \"Canfam_GSD: De novo chromosome-length genome assembly of the German Shepherd Dog (Canis lupus familiaris) using a combination of long reads, optical mapping, and Hi-C\"

This is the open peer reviewers comments and recommendations regarding the submitted GigaScience article and/or dataset.

Peer review of \"ShinyLearner: A containerized benchmarking tool for machine-learning classification of tabular data\"

Stephen Eglen
This is the open peer reviewers comments and recommendations regarding the submitted GigaScience article and/or dataset.

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