http://www.gigadb.org en-us Tue, 26 Jun 2018 08:46:51 +0000 http://gigadb.org/dataset/100462 Mon, 25 Jun 2018 00:00:00 +0000 Porites rus from a hologenomic sample, and compared it to traditional approaches.
Our results demonstrate that binning performs well for hologenomic data, producing sufficient reads for assembling the draft genome of P. rus. An assembly evaluation based on operational criteria showed comparable results to symbiont-free approaches in terms of completeness and usefulness, despite a high degree of fragmentation in our assembly. In addition, we found that binning provides sufficient data for exploratory k-mer estimation of genomic features, such as genome size and heterozygosity.
Binning constitutes a powerful approach for disentangling taxonomically complex coral hologenomes. Considering the recent decline of coral reefs on the one hand and previous limitations to coral genome sequencing on the other hand, binning may facilitate rapid and reliable genome assembly. This study also provides an important milestone in advancing binning from the metagenomic to the hologenomic and from the prokaryotic to the eukaryotic level. ]]> http://gigadb.org/dataset/100473 Thu, 21 Jun 2018 00:00:00 +0000 http://gigadb.org/dataset/100468 Tue, 19 Jun 2018 00:00:00 +0000 We demonstrate that hot-starting, from containers that have been frozen after the application has already begun execution, can speed up bioinformatics workflows by avoiding repetitive initialization steps. We use an open source tool called Checkpoint and Restore in Userspace (CRIU) to save the state of the containers as a collection of checkpoint files on disk after it has read in the indices. The resulting checkpoint files are migrated to the host and CRIU is used to regenerate the containers in that ready-to-run hot-start state. As a proof-of-concept example, we create a hot-start container for the STAR aligner and deploy this container to align RNA sequencing data. We compare the performance of the alignment step with and without checkpoints on cloud platforms using local and network disks.
We demonstrate that hot-starting Docker containers from snapshots taken after repetitive initialization steps are completed, significantly speeds up the execution of the STAR aligner on all experimental platforms, including Amazon Web Services (AWS), Microsoft Azure and local virtual machines. Our method can be potentially employed in other bioinformatics applications in which a checkpoint can be inserted after a repetitive initialization phase. ]]> http://gigadb.org/dataset/100463 Tue, 19 Jun 2018 00:00:00 +0000 http://gigadb.org/dataset/100476 Tue, 19 Jun 2018 00:00:00 +0000 http://gigadb.org/dataset/100471 Fri, 15 Jun 2018 00:00:00 +0000 We have developed a similarity-based approach that matches individuals to subjects with similar conditions. We modeled the disease with a Gaussian process, and tested the method in the Alzheimer's Disease Big Data DREAM Challenge. Ranked the highest among submitted methods, our diagnostic model predicted cognitive impairment scores in an independent dataset test with a correlation score of 0.573. It differentiated Alzheimer's disease patients from control subjects with an area under receiver operating curve of 0.920. Without knowing longitudial information about subjects, the model predicted patients that are vulnerable to MCI-to-AD conversion through the similarity network. This diagnostic framework can be applied to other diseases with clinical heterogeneity, such as Parkinson's disease. ]]> http://gigadb.org/dataset/100457 Mon, 11 Jun 2018 00:00:00 +0000 http://gigadb.org/dataset/100466 Fri, 08 Jun 2018 00:00:00 +0000 A total of 64.72 gigabases (Gb) of raw PacBio Sequel reads were generated from four 20 kb libraries. After filtering, 64.53 Gb of clean reads were obtained, giving 72.59 × coverage depth. Assembly using Canu gave an assembly length of 823.74 Mb, with a contig N50 of 2.76 Mb. The final size of the assembled A. nanus genome was close to the 889 Mb estimated by k-mer analysis. The gene annotation completeness was evaluated by BUSCO, and 1,327 out of the 1,440 conserved genes (92.15%) could be found in the A. nanus assembly. Genome annotation revealed that 74.08% of the A. nanus genome is composed of repetitive elements, and 53.44% of long terminal repeat elements (LTRs). We predicted 37,188 protein-coding genes, of which 96.53% were functionally annotated.
The genomic sequences of A. nanus could be a valuable source for comparative genomic analysis in the legume family, and will be useful for understanding the phylogenetic relationships of the Thermopsideae and the evolutionary response of plant species to the Qinghai Tibetan Plateau uplift. ]]> http://gigadb.org/dataset/100433 Fri, 08 Jun 2018 00:00:00 +0000 We first sequenced and de novo assembled a 465.24 Mb genome for the B. splendens variety Giant, with a weighted average (N50) scaffold size of 949.03 Kb and an N50 contig size of 19.01 Kb, covering 99.93% of the estimated genome size. To obtain a chromosome-level genome assembly, we constructed one Hi-C library and sequenced 75.24 Gb reads using the BGISEQ-500 platform. We anchored approximately 93% of the scaffold sequences into 21 chromosomes and evaluated the quality of our assembly using the high contact frequency heatmap and BUSCO. We also performed comparative chromosome analyses between Oryzias latipes and B. splendens, revealing a chromosome conservation evolution in B. splendens. We predicted a total of 23,981 genes assisted by RNA-seq data generated from brain, liver, muscle and heart tissues of Giant, and annotated 15% repetitive sequences in the genome. Additionally, we resequenced other five B. splendens varieties and detected ~3.4M single-nucleotide variations (SNVs) and 27,305 indels.
We provide the first chromosome-level genome for the Siamese fighting fish. The genome will lay a valuable foundation for future research on aggression in B. splendens. ]]> http://gigadb.org/dataset/100454 Thu, 07 Jun 2018 00:00:00 +0000 GitHub. ]]>