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https://www.readbyqxmd.com/read/30523036/minerva-an-alignment-and-reference-free-approach-to-deconvolve-linked-reads-for-metagenomics
#1
David Danko, Dmitry Meleshko, Daniela Bezdan, Christopher Mason, Iman Hajirasouliha
Emerging Linked-Read technologies (aka Read-Cloud or barcoded short-reads) have revived interest in short-read technology as a viable way to understand large-scale structure in genomes and metagenomes. Linked-Read technologies, such as the 10x Chromium system, use a microfluidic system and a specialized set of 3' barcodes (aka UIDs) to tag short DNA reads sourced from the same long fragment of DNA; subsequently, the tagged reads are sequenced on standard short read platforms. This approach results in interesting compromises...
December 6, 2018: Genome Research
https://www.readbyqxmd.com/read/30510133/advantages-of-single-nucleus-over-single-cell-rna-sequencing-of-adult-kidney-rare-cell-types-and-novel-cell-states-revealed-in-fibrosis
#2
Haojia Wu, Yuhei Kirita, Erinn L Donnelly, Benjamin D Humphreys
BACKGROUND: A challenge for single-cell genomic studies in kidney and other solid tissues is generating a high-quality single-cell suspension that contains rare or difficult-to-dissociate cell types and is free of both RNA degradation and artifactual transcriptional stress responses. METHODS: We compared single-cell RNA sequencing (scRNA-seq) using the DropSeq platform with single-nucleus RNA sequencing (snRNA-seq) using sNuc-DropSeq, DroNc-seq, and 10X Chromium platforms on adult mouse kidney...
December 3, 2018: Journal of the American Society of Nephrology: JASN
https://www.readbyqxmd.com/read/30472192/comparative-analysis-of-droplet-based-ultra-high-throughput-single-cell-rna-seq-systems
#3
Xiannian Zhang, Tianqi Li, Feng Liu, Yaqi Chen, Jiacheng Yao, Zeyao Li, Yanyi Huang, Jianbin Wang
Since its establishment in 2009, single-cell RNA sequencing (RNA-seq) has been a major driver behind progress in biomedical research. In developmental biology and stem cell studies, the ability to profile single cells confers particular benefits. Although most studies still focus on individual tissues or organs, the recent development of ultra-high-throughput single-cell RNA-seq has demonstrated potential power in characterizing more complex systems or even the entire body. However, although multiple ultra-high-throughput single-cell RNA-seq systems have attracted attention, no systematic comparison of these systems has been performed...
November 16, 2018: Molecular Cell
https://www.readbyqxmd.com/read/30367597/tigmint-correcting-assembly-errors-using-linked-reads-from-large-molecules
#4
Shaun D Jackman, Lauren Coombe, Justin Chu, Rene L Warren, Benjamin P Vandervalk, Sarah Yeo, Zhuyi Xue, Hamid Mohamadi, Joerg Bohlmann, Steven J M Jones, Inanc Birol
BACKGROUND: Genome sequencing yields the sequence of many short snippets of DNA (reads) from a genome. Genome assembly attempts to reconstruct the original genome from which these reads were derived. This task is difficult due to gaps and errors in the sequencing data, repetitive sequence in the underlying genome, and heterozygosity. As a result, assembly errors are common. In the absence of a reference genome, these misassemblies may be identified by comparing the sequencing data to the assembly and looking for discrepancies between the two...
October 26, 2018: BMC Bioinformatics
https://www.readbyqxmd.com/read/30355765/highly-continuous-genome-assembly-of-eurasian-perch-perca-fluviatilis-using-linked-read-sequencing
#5
Mikhail Yu Ozerov, Freed Ahmad, Riho Gross, Lilian Pukk, Siim Kahar, Veljo Kisand, Anti Vasemägi
The Eurasian perch ( Perca fluviatilis ) is the most common fish of the Percidae family and is widely distributed across Eurasia. Perch is a popular target for professional and recreational fisheries, and a promising freshwater aquaculture species in Europe. However, despite its high ecological, economical and societal importance, the available genomic resources for P. fluviatilis are rather limited. In this work, we report de novo assembly and annotation of the whole genome sequence of perch. The linked-read based technology with 10X Genomics Chromium chemistry and Supernova assembler produced a draft perch genome ~1...
October 24, 2018: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/30346553/cost-effective-assembly-of-the-african-wild-dog-lycaon-pictus-genome-using-linked-reads
#6
Ellie E Armstrong, Ryan W Taylor, Stefan Prost, Peter Blinston, Esther van der Meer, Hillary Madzikanda, Olivia Mufute, Roseline Mandisodza-Chikerema, John Stuelpnagel, Claudio Sillero-Zubiri, Dmitri Petrov
Background: A high-quality reference genome assembly is a valuable tool for the study of non-model organisms. Genomic techniques can provide important insights about past population sizes, local adaptation, and aid in the development of breeding management plans. This information is important for fields like conservation genetics, where endangered species require critical and immediate attention. However, funding for genomic-based methods can be sparse for conservation projects, as costs for general species management can consume budgets...
October 22, 2018: GigaScience
https://www.readbyqxmd.com/read/30275930/new-chromosome-counts-and-genome-size-estimates-for-28-species-of-taraxacum-sect-taraxacum
#7
Petra Macháčková, Ľuboš Majeský, Michal Hroneš, Eva Hřibová, Bohumil Trávníček, Radim J Vašut
The species-rich and widespread genus Taraxacum F. H. Wiggers, 1780 (Asteraceae subfamily Cichorioideae) is one of the most taxonomically complex plant genera in the world, mainly due to its combination of different sexual and asexual reproduction strategies. Polyploidy is usually confined to apomictic microspecies, varying from 3x to 6x (rarely 10x). In this study, we focused on Taraxacum sect. Taraxacum (= T.sect.Ruderalia; T.officinale group), i.e., the largest group within the genus. We counted chromosome numbers and measured the DNA content for species sampled in Central Europe, mainly in Czechia...
2018: Comparative Cytogenetics
https://www.readbyqxmd.com/read/30247488/a-universal-snp-and-small-indel-variant-caller-using-deep-neural-networks
#8
Ryan Poplin, Pi-Chuan Chang, David Alexander, Scott Schwartz, Thomas Colthurst, Alexander Ku, Dan Newburger, Jojo Dijamco, Nam Nguyen, Pegah T Afshar, Sam S Gross, Lizzie Dorfman, Cory Y McLean, Mark A DePristo
Despite rapid advances in sequencing technologies, accurately calling genetic variants present in an individual genome from billions of short, errorful sequence reads remains challenging. Here we show that a deep convolutional neural network can call genetic variation in aligned next-generation sequencing read data by learning statistical relationships between images of read pileups around putative variant and true genotype calls. The approach, called DeepVariant, outperforms existing state-of-the-art tools...
November 2018: Nature Biotechnology
https://www.readbyqxmd.com/read/30228881/comparison-of-clustering-tools-in-r-for-medium-sized-10x-genomics-single-cell-rna-sequencing-data
#9
Saskia Freytag, Luyi Tian, Ingrid Lönnstedt, Milica Ng, Melanie Bahlo
Background: The commercially available 10x Genomics protocol to generate droplet-based single-cell RNA-seq (scRNA-seq) data is enjoying growing popularity among researchers. Fundamental to the analysis of such scRNA-seq data is the ability to cluster similar or same cells into non-overlapping groups. Many competing methods have been proposed for this task, but there is currently little guidance with regards to which method to use. Methods: Here we use one gold standard 10x Genomics dataset, generated from the mixture of three cell lines, as well as three silver standard 10x Genomics datasets generated from peripheral blood mononuclear cells to examine not only the accuracy but also robustness of a dozen methods...
2018: F1000Research
https://www.readbyqxmd.com/read/30138581/statistical-binning-for-barcoded-reads-improves-downstream-analyses
#10
Ariya Shajii, Ibrahim Numanagić, Christopher Whelan, Bonnie Berger
Sequencing technologies are capturing longer-range genomic information at lower error rates, enabling alignment to genomic regions that are inaccessible with short reads. However, many methods are unable to align reads to much of the genome, recognized as important in disease, and thus report erroneous results in downstream analyses. We introduce EMA, a novel two-tiered statistical binning model for barcoded read alignment, that first probabilistically maps reads to potentially multiple "read clouds" and then within clouds by newly exploiting the non-uniform read densities characteristic of barcoded read sequencing...
August 22, 2018: Cell Systems
https://www.readbyqxmd.com/read/30124856/draft-genome-of-glyptosternon-maculatum-an-endemic-fish-from-tibet-plateau
#11
Haiping Liu, Qiyong Liu, Zhiqiang Chen, Yanchao Liu, Chaowei Zhou, Qiqi Liang, Caixia Ma, Jianshe Zhou, Yingzi Pan, Meiqun Chen, Wangjiu, Wenkai Jiang, Shijun Xiao, Zhenbo Mou
Background: Mechanisms for high-altitude adaption have attracted widespread interest among evolutionary biologists. Several genome-wide studies have been carried out for endemic vertebrates in Tibet, including mammals, birds, and amphibians. However, little information is available about the adaptive evolution of highland fishes. Glyptosternon maculatum (Regan 1905), also known as Regan or barkley and endemic to the Tibetan Plateau, belongs to the Sisoridae family, order Siluriformes (catfishes)...
September 1, 2018: GigaScience
https://www.readbyqxmd.com/read/30061114/single-cell-rna-seq-analysis-identifies-markers-of-resistance-to-targeted-braf-inhibitors-in-melanoma-cell-populations
#12
Yu-Jui Ho, Naishitha Anaparthy, David Molik, Grinu Mathew, Toby Aicher, Ami Patel, James Hicks, Molly Gale Hammell
Single-cell RNA-seq's (scRNA-seq) unprecedented cellular resolution at a genome-wide scale enables us to address questions about cellular heterogeneity that are inaccessible using methods that average over bulk tissue extracts. However, scRNA-seq data sets also present additional challenges such as high transcript dropout rates, stochastic transcription events, and complex population substructures. Here, we present a <u>s</u>ingle-cell RNA-seq <u>a</u>nalysis and <u>k</u>lustering <u>e</u>valuation (SAKE), a robust method for scRNA-seq analysis that provides quantitative statistical metrics at each step of the analysis pipeline...
September 2018: Genome Research
https://www.readbyqxmd.com/read/29991676/detection-and-removal-of-barcode-swapping-in-single-cell-rna-seq-data
#13
Jonathan A Griffiths, Arianne C Richard, Karsten Bach, Aaron T L Lun, John C Marioni
Barcode swapping results in the mislabelling of sequencing reads between multiplexed samples on patterned flow-cell Illumina sequencing machines. This may compromise the validity of numerous genomic assays; however, the severity and consequences of barcode swapping remain poorly understood. We have used two statistical approaches to robustly quantify the fraction of swapped reads in two plate-based single-cell RNA-sequencing datasets. We found that approximately 2.5% of reads were mislabelled between samples on the HiSeq 4000, which is lower than previous reports...
July 10, 2018: Nature Communications
https://www.readbyqxmd.com/read/29914369/hapdenovo-a-haplotype-based-approach-for-filtering-and-phasing-de-novo-mutations-in-linked-read-sequencing-data
#14
Xin Zhou, Serafim Batzoglou, Arend Sidow, Lu Zhang
BACKGROUND: De novo mutations (DNMs) are associated with neurodevelopmental and congenital diseases, and their detection can contribute to understanding disease pathogenicity. However, accurate detection is challenging because of their small number relative to the genome-wide false positives in next generation sequencing (NGS) data. Software such as DeNovoGear and TrioDeNovo have been developed to detect DNMs, but at good sensitivity they still produce many false positive calls. RESULTS: To address this challenge, we develop HAPDeNovo, a program that leverages phasing information from linked read sequencing, to remove false positive DNMs from candidate lists generated by DNM-detection tools...
June 18, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29792160/nextsv-a-meta-caller-for-structural-variants-from-low-coverage-long-read-sequencing-data
#15
Li Fang, Jiang Hu, Depeng Wang, Kai Wang
BACKGROUND: Structural variants (SVs) in human genomes are implicated in a variety of human diseases. Long-read sequencing delivers much longer read lengths than short-read sequencing and may greatly improve SV detection. However, due to the relatively high cost of long-read sequencing, it is unclear what coverage is needed and how to optimally use the aligners and SV callers. RESULTS: In this study, we developed NextSV, a meta-caller to perform SV calling from low coverage long-read sequencing data...
May 23, 2018: BMC Bioinformatics
https://www.readbyqxmd.com/read/29608694/scanpav-a-pipeline-for-extracting-presence-absence-variations-in-genome-pairs
#16
Francesca Giordano, Maximilian R Stammnitz, Elizabeth P Murchison, Zemin Ning
Motivation: The recent technological advances in genome sequencing techniques have resulted in an exponential increase in the number of sequenced human and non-human genomes. The ever increasing number of assemblies generated by novel de novo pipelines and strategies demands the development of new software to evaluate assembly quality and completeness. One way to determine the completeness of an assembly is by detecting its Presence-Absence variations (PAV) with respect to a reference, where PAVs between two assemblies are defined as the sequences present in one assembly but entirely missing in the other one...
September 1, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29491155/copy-number-heterogeneity-large-origin-tandem-repeats-and-interspecies-recombination-in-human-herpesvirus-6a-hhv-6a-and-hhv-6b-reference-strains
#17
Alexander L Greninger, Pavitra Roychoudhury, Negar Makhsous, Derek Hanson, Jill Chase, Gerhard Krueger, Hong Xie, Meei-Li Huang, Lindsay Saunders, Dharam Ablashi, David M Koelle, Linda Cook, Keith R Jerome
Quantitative PCR is a diagnostic pillar for clinical virology testing, and reference materials are necessary for accurate, comparable quantitation between clinical laboratories. Accurate quantitation of human herpesvirus 6A/B (HHV-6A/B) is important for detection of viral reactivation and inherited chromosomally integrated HHV-6A/B in immunocompromised patients. Reference materials in clinical virology commonly consist of laboratory-adapted viral strains that may be affected by the culture process. We performed next-generation sequencing to make relative copy number measurements at single nucleotide resolution of eight candidate HHV-6A and seven HHV-6B reference strains and DNA materials from the HHV-6 Foundation and Advanced Biotechnologies Inc...
May 15, 2018: Journal of Virology
https://www.readbyqxmd.com/read/29360925/recurrent-hyperactive-esr1-fusion-proteins-in-endocrine-therapy-resistant-breast-cancer
#18
R J Hartmaier, S E Trabucco, N Priedigkeit, J H Chung, C A Parachoniak, P Vanden Borre, S Morley, M Rosenzweig, L M Gay, M E Goldberg, J Suh, S M Ali, J Ross, B Leyland-Jones, B Young, C Williams, B Park, M Tsai, B Haley, J Peguero, R D Callahan, I Sachelarie, J Cho, J M Atkinson, A Bahreini, A M Nagle, S L Puhalla, R J Watters, Z Erdogan-Yildirim, L Cao, S Oesterreich, A Mathew, P C Lucas, N E Davidson, A M Brufsky, G M Frampton, P J Stephens, J Chmielecki, A V Lee
Background: Estrogen receptor-positive (ER-positive) metastatic breast cancer is often intractable due to endocrine therapy resistance. Although ESR1 promoter switching events have been associated with endocrine-therapy resistance, recurrent ESR1 fusion proteins have yet to be identified in advanced breast cancer. Patients and methods: To identify genomic structural rearrangements (REs) including gene fusions in acquired resistance, we undertook a multimodal sequencing effort in three breast cancer patient cohorts: (i) mate-pair and/or RNAseq in 6 patient-matched primary-metastatic tumors and 51 metastases, (ii) high coverage (>500×) comprehensive genomic profiling of 287-395 cancer-related genes across 9542 solid tumors (5216 from metastatic disease), and (iii) ultra-high coverage (>5000×) genomic profiling of 62 cancer-related genes in 254 ctDNA samples...
April 1, 2018: Annals of Oncology: Official Journal of the European Society for Medical Oncology
https://www.readbyqxmd.com/read/29356894/development-of-thinopyrum-ponticum-specific-molecular-markers-and-fish-probes-based-on-slaf-seq-technology
#19
Liqin Liu, Qiaoling Luo, Wan Teng, Bin Li, Hongwei Li, Yiwen Li, Zhensheng Li, Qi Zheng
Based on SLAF-seq, 67 Thinopyrum ponticum-specific markers and eight Th. ponticum-specific FISH probes were developed, and these markers and probes could be used for detection of alien chromatin in a wheat background. Decaploid Thinopyrum ponticum (2n = 10x = 70) is a valuable gene reservoir for wheat improvement. Identification of Th. ponticum introgression would facilitate its transfer into diverse wheat genetic backgrounds and its practical utilization in wheat improvement. Based on specific-locus-amplified fragment sequencing (SLAF-seq) technology, 67 new Th...
May 2018: Planta
https://www.readbyqxmd.com/read/29204149/diversity-in-grain-amaranths-and-relatives-distinguished-by-genotyping-by-sequencing-gbs
#20
Xingbo Wu, Matthew W Blair
The genotyping by sequencing (GBS) method has become a molecular marker technology of choice for many crop plants because of its simultaneous discovery and evaluation of a large number of single nucleotide polymorphisms (SNPs) and utility for germplasm characterization. Genome representation and complexity reduction are the basis for GBS fingerprinting and can vary by species based on genome size and other sequence characteristics. Grain amaranths are a set of three species that were domesticated in the New World to be high protein, pseudo-cereal grain crops...
2017: Frontiers in Plant Science
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