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https://www.readbyqxmd.com/read/28407084/comparative-analysis-of-de-novo-assemblers-for-variation-discovery-in-personal-genomes
#1
Shulan Tian, Huihuang Yan, Eric W Klee, Michael Kalmbach, Susan L Slager
Current variant discovery approaches often rely on an initial read mapping to the reference sequence. Their effectiveness is limited by the presence of gaps, potential misassemblies, regions of duplicates with a high-sequence similarity and regions of high-sequence divergence in the reference. Also, mapping-based approaches are less sensitive to large INDELs and complex variations and provide little phase information in personal genomes. A few de novo assemblers have been developed to identify variants through direct variant calling from the assembly graph, micro-assembly and whole-genome assembly, but mainly for whole-genome sequencing (WGS) data...
April 11, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/28286147/evaluation-and-assessment-of-read-mapping-by-multiple-next-generation-sequencing-aligners-based-on-genome-wide-characteristics
#2
Subazini Thankaswamy-Kosalai, Partho Sen, Intawat Nookaew
Massive data produced due to the advent of next-generation sequencing (NGS) technology is widely used for biological researches and medical diagnosis. The crucial step in NGS analysis is read alignment or mapping which is computationally intensive and complex. The mapping bias tends to affect the downstream analysis, including detection of polymorphisms. In order to provide guidelines to the biologist for suitable selection of aligners; we have evaluated and benchmarked 5 different aligners (BWA, Bowtie2, NovoAlign, Smalt and Stampy) and their mapping bias based on characteristics of 5 microbial genomes...
March 9, 2017: Genomics
https://www.readbyqxmd.com/read/28249565/statistical-method-to-compare-massive-parallel-sequencing-pipelines
#3
M H Elsensohn, N Leblay, S Dimassi, A Campan-Fournier, A Labalme, F Roucher-Boulez, D Sanlaville, G Lesca, C Bardel, P Roy
BACKGROUND: Today, sequencing is frequently carried out by Massive Parallel Sequencing (MPS) that cuts drastically sequencing time and expenses. Nevertheless, Sanger sequencing remains the main validation method to confirm the presence of variants. The analysis of MPS data involves the development of several bioinformatic tools, academic or commercial. We present here a statistical method to compare MPS pipelines and test it in a comparison between an academic (BWA-GATK) and a commercial pipeline (TMAP-NextGENe®), with and without reference to a gold standard (here, Sanger sequencing), on a panel of 41 genes in 43 epileptic patients...
March 1, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28155631/a-fast-read-alignment-method-based-on-seed-and-vote-for-next-generation-sequencing
#4
Song Liu, Yi Wang, Fei Wang
BACKGROUND: The next-generation of sequencing technologies, along with the development of bioinformatics, are generating a growing number of reads every day. For the convenience of further research, these reads should be aligned to the reference genome by read alignment tools. Despite the diversity of read alignment tools, most have no comprehensive advantage in both accuracy and speed. For example, BWA has comparatively high accuracy, but its speed leaves much to be desired, becoming a bottleneck while an increasing number of reads need to be aligned every day...
December 23, 2016: BMC Bioinformatics
https://www.readbyqxmd.com/read/28118849/distinguishing-potential-bacteria-tumor-associations-from-contamination-in-a-secondary-data-analysis-of-public-cancer-genome-sequence-data
#5
Kelly M Robinson, Jonathan Crabtree, John S A Mattick, Kathleen E Anderson, Julie C Dunning Hotopp
BACKGROUND: A variety of bacteria are known to influence carcinogenesis. Therefore, we sought to investigate if publicly available whole genome and whole transcriptome sequencing data generated by large public cancer genome efforts, like The Cancer Genome Atlas (TCGA), could be used to identify bacteria associated with cancer. The Burrows-Wheeler aligner (BWA) was used to align a subset of Illumina paired-end sequencing data from TCGA to the human reference genome and all complete bacterial genomes in the RefSeq database in an effort to identify bacterial read pairs from the microbiome...
January 25, 2017: Microbiome
https://www.readbyqxmd.com/read/28065898/metaspark-a-spark-based-distributed-processing-tool-to-recruit-metagenomic-reads-to-reference-genomes
#6
Wei Zhou, Ruilin Li, Shuo Yuan, ChangChun Liu, Shaowen Yao, Jing Luo, Beifang Niu
Summary: With the advent of next-generation sequencing, traditional bioinformatics tools are challenged by massive raw metagenomic datasets. One of the bottlenecks of metagenomic studies is lack of large-scale and cloud computing suitable data analysis tools. In this paper, we proposed a Spark based tool, called MetaSpark, to recruit metagenomic reads to reference genomes. MetaSpark benefits from the distributed data set (RDD) of Spark, which makes it able to cache data set in memory across cluster nodes and scale well with the datasets...
April 1, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28011768/seqlib-a-c%C3%A2-api-for-rapid-bam-manipulation-sequence-alignment-and-sequence-assembly
#7
Jeremiah Wala, Rameen Beroukhim
We present SeqLib, a C ++ API and command line tool that provides a rapid and user-friendly interface to BAM/SAM/CRAM files, global sequence alignment operations and sequence assembly. Four C libraries perform core operations in SeqLib: HTSlib for BAM access, BWA-MEM and BLAT for sequence alignment and Fermi for error correction and sequence assembly. Benchmarking indicates that SeqLib has lower CPU and memory requirements than leading C ++ sequence analysis APIs. We demonstrate an example of how minimal SeqLib code can extract, error-correct and assemble reads from a CRAM file and then align with BWA-MEM...
March 1, 2017: Bioinformatics
https://www.readbyqxmd.com/read/27928499/whole-genome-resequencing-of-a-laboratory-adapted-drosophila-melanogaster%C3%A2-population-sample
#8
William P Gilks, Tanya M Pennell, Ilona Flis, Matthew T Webster, Edward H Morrow
As part of a study into the molecular genetics of sexually dimorphic complex traits, we used high-throughput sequencing to obtain data on genomic variation in an outbred laboratory-adapted fruit fly ( Drosophila melanogaster) population. We successfully resequenced the whole genome of 220 hemiclonal females that were heterozygous for the same Berkeley reference line genome (BDGP6/dm6), and a unique haplotype from the outbred base population (LH M). The use of a static and known genetic background enabled us to obtain sequences from whole-genome phased haplotypes...
2016: F1000Research
https://www.readbyqxmd.com/read/27912743/str-realigner-a-realignment-method-for-short-tandem-repeat-regions
#9
Kaname Kojima, Yosuke Kawai, Kazuharu Misawa, Takahiro Mimori, Masao Nagasaki
BACKGROUND: In the estimation of repeat numbers in a short tandem repeat (STR) region from high-throughput sequencing data, two types of strategies are mainly taken: a strategy based on counting repeat patterns included in sequence reads spanning the region and a strategy based on estimating the difference between the actual insert size and the insert size inferred from paired-end reads. The quality of sequence alignment is crucial, especially in the former approaches although usual alignment methods have difficulty in STR regions due to insertions and deletions caused by the variations of repeat numbers...
December 3, 2016: BMC Genomics
https://www.readbyqxmd.com/read/27824716/ridge-dimensions-of-the-edentulous-mandible-in-posterior-sextants-an-observational-study-on-cone-beam-computed-tomography-radiographs
#10
Eriberto Bressan, Nadia Ferrarese, Mattia Pramstraller, Diego Lops, Roberto Farina, Cristiano Tomasi
AIMS: To evaluate the ridge dimensions of posterior sextant in totally edentulous mandibles. MATERIAL AND METHODS: Cone beam computed tomography scans of 136 patients were retrospectively included for analysis. At sites corresponding to the second premolar (site a) and the mesial and distal root of first molar (sites b and c, respectively), bone height (BH) and bone width (BW) were measured. RESULTS: BH significantly decreased from site a (11...
February 2017: Implant Dentistry
https://www.readbyqxmd.com/read/27780227/climate-risk-modelling-of-balsam-woolly-adelgid-damage-severity-in-subalpine-fir-stands-of-western-north-america
#11
Kathryn H Hrinkevich, Robert A Progar, David C Shaw
The balsam woolly adelgid (Adelges piceae (Ratzeburg) (Homoptera: Adelgidae)) (BWA) is a nonnative, invasive insect that threatens Abies species throughout North America. It is well established in the Pacific Northwest, but continues to move eastward through Idaho and into Montana and potentially threatens subalpine fir to the south in the central and southern Rocky Mountains. We developed a climatic risk model and map that predicts BWA impacts to subalpine fir using a two-step process. Using 30-year monthly climate normals from sites with quantitatively derived BWA damage severity index values, we built a regression model that significantly explained insect damage...
2016: PloS One
https://www.readbyqxmd.com/read/27769321/single-exome-sequencing-identified-a-novel-rp2-mutation-in-a-child-with-x-linked-retinitis-pigmentosa
#12
Hassol Lim, Young-Mi Park, Jong-Keuk Lee, Hyun Taek Lim
OBJECTIVE: To present an efficient and successful application of a single-exome sequencing study in a family clinically diagnosed with X-linked retinitis pigmentosa. DESIGN: Exome sequencing study based on clinical examination data. PARTICIPANTS: An 8-year-old proband and his family. METHODS: The proband and his family members underwent comprehensive ophthalmologic examinations. Exome sequencing was undertaken in the proband using Agilent SureSelect Human All Exon Kit and Illumina HiSeq 2000 platform...
October 2016: Canadian Journal of Ophthalmology. Journal Canadien D'ophtalmologie
https://www.readbyqxmd.com/read/27764769/establishing-the-involvement-of-the-novel-gene-agbl5-in-retinitis-pigmentosa-by-whole-genome-sequencing
#13
Kari Branham, Hiroko Matsui, Pooja Biswas, Aditya A Guru, Michael Hicks, John J Suk, He Li, David Jakubosky, Tao Long, Amalio Telenti, Naoki Nariai, John R Heckenlively, Kelly A Frazer, Paul A Sieving, Radha Ayyagari
While more than 250 genes are known to cause inherited retinal degenerations (IRD), nearly 40-50% of families have the genetic basis for their disease unknown. In this study we sought to identify the underlying cause of IRD in a family by whole genome sequence (WGS) analysis. Clinical characterization including standard ophthalmic examination, fundus photography, visual field testing, electroretinography, and review of medical and family history was performed. WGS was performed on affected and unaffected family members using Illumina HiSeq X10...
December 1, 2016: Physiological Genomics
https://www.readbyqxmd.com/read/27741057/influence-of-rest-intervals-after-assisted-sprinting-on-bodyweight-sprint-times-in-female-collegiate-soccer-players
#14
Austyn L Nealer, Dustin D Dunnick, Kylie K Malyszek, Megan A Wong, Pablo B Costa, Jared W Coburn, Lee E Brown
Nealer, AL, Dunnick, DD, Malyszek, KK, Wong, MA, Costa, PB, Coburn, JW, and Brown, LE. Influence of rest intervals after assisted sprinting on bodyweight sprint times in female collegiate soccer players. J Strength Cond Res 31(1): 88-94, 2017-Speed is a crucial element an athlete must possess to be successful. In soccer, the ability to accelerate faster than your opponent can result in being first to reach a ball on a breakaway or stopping a counter attack. A unique way to train explosive movements is to evoke postactivation potentiation (PAP) in the working muscles...
January 2017: Journal of Strength and Conditioning Research
https://www.readbyqxmd.com/read/27716037/impact-of-post-alignment-processing-in-variant-discovery-from-whole-exome-data
#15
Shulan Tian, Huihuang Yan, Michael Kalmbach, Susan L Slager
BACKGROUND: GATK Best Practices workflows are widely used in large-scale sequencing projects and recommend post-alignment processing before variant calling. Two key post-processing steps include the computationally intensive local realignment around known INDELs and base quality score recalibration (BQSR). Both have been shown to reduce erroneous calls; however, the findings are mainly supported by the analytical pipeline that incorporates BWA and GATK UnifiedGenotyper. It is not known whether there is any benefit of post-processing and to what extent the benefit might be for pipelines implementing other methods, especially given that both mappers and callers are typically updated...
October 3, 2016: BMC Bioinformatics
https://www.readbyqxmd.com/read/27613752/suitability-of-different-mapping-algorithms-for-genome-wide-polymorphism-scans-with-pool-seq-data
#16
Robert Kofler, Anna Maria Langmüller, Pierre Nouhaud, Kathrin Anna Otte, Christian Schlötterer
The cost-effectiveness of sequencing pools of individuals (Pool-Seq) provides the basis for the popularity and wide-spread use of this method for many research questions, ranging from unravelling the genetic basis of complex traits to the clonal evolution of cancer cells. Because the accuracy of Pool-Seq could be affected by many potential sources of error, several studies determined, for example, the influence of the sequencing technology, the library preparation protocol, and mapping parameters. Nevertheless, the impact of the mapping tools has not yet been evaluated...
September 9, 2016: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/27606429/single-nucleotide-polymorphism-discovery-in-bovine-pituitary-gland-using-rna-seq-technology
#17
Chandra Shekhar Pareek, Rafał Smoczyński, Haja N Kadarmideen, Piotr Dziuba, Paweł Błaszczyk, Marcin Sikora, Paulina Walendzik, Tomasz Grzybowski, Mariusz Pierzchała, Jarosław Horbańczuk, Agnieszka Szostak, Magdalena Ogluszka, Lech Zwierzchowski, Urszula Czarnik, Leyland Fraser, Przemysław Sobiech, Krzysztof Wąsowicz, Brian Gelfand, Yaping Feng, Dibyendu Kumar
Examination of bovine pituitary gland transcriptome by strand-specific RNA-seq allows detection of putative single nucleotide polymorphisms (SNPs) within potential candidate genes (CGs) or QTLs regions as well as to understand the genomics variations that contribute to economic trait. Here we report a breed-specific model to successfully perform the detection of SNPs in the pituitary gland of young growing bulls representing Polish Holstein-Friesian (HF), Polish Red, and Hereford breeds at three developmental ages viz...
2016: PloS One
https://www.readbyqxmd.com/read/27604516/from-wet-lab-to-variations-concordance-and-speed-of-bioinformatics-pipelines-for-whole-genome-and-whole-exome-sequencing
#18
Steve Laurie, Marcos Fernandez-Callejo, Santiago Marco-Sola, Jean-Remi Trotta, Jordi Camps, Alejandro Chacón, Antonio Espinosa, Marta Gut, Ivo Gut, Simon Heath, Sergi Beltran
As whole genome sequencing becomes cheaper and faster, it will progressively substitute targeted next-generation sequencing as standard practice in research and diagnostics. However, computing cost-performance ratio is not advancing at an equivalent rate. Therefore, it is essential to evaluate the robustness of the variant detection process taking into account the computing resources required. We have benchmarked six combinations of state-of-the-art read aligners (BWA-MEM and GEM3) and variant callers (FreeBayes, GATK HaplotypeCaller, SAMtools) on whole genome and whole exome sequencing data from the NA12878 human sample...
December 2016: Human Mutation
https://www.readbyqxmd.com/read/27562535/transcriptomic-snp-discovery-for-custom-genotyping-arrays-impacts-of-sequence-data-snp-calling-method-and-genotyping-technology-on-the-probability-of-validation-success
#19
Emily Humble, Michael A S Thorne, Jaume Forcada, Joseph I Hoffman
BACKGROUND: Single nucleotide polymorphism (SNP) discovery is an important goal of many studies. However, the number of 'putative' SNPs discovered from a sequence resource may not provide a reliable indication of the number that will successfully validate with a given genotyping technology. For this it may be necessary to account for factors such as the method used for SNP discovery and the type of sequence data from which it originates, suitability of the SNP flanking sequences for probe design, and genomic context...
August 26, 2016: BMC Research Notes
https://www.readbyqxmd.com/read/27538485/res-scanner-a-software-package-for-genome-wide-identification-of-rna-editing-sites
#20
Zongji Wang, Jinmin Lian, Qiye Li, Pei Zhang, Yang Zhou, Xiaoyu Zhan, Guojie Zhang
BACKGROUND: High-throughput sequencing (HTS) provides a powerful solution for the genome-wide identification of RNA-editing sites. However, it remains a great challenge to distinguish RNA-editing sites from genetic variants and technical artifacts caused by sequencing or read-mapping errors. RESULTS: Here we present RES-Scanner, a flexible and efficient software package that detects and annotates RNA-editing sites using matching RNA-seq and DNA-seq data from the same individuals or samples...
2016: GigaScience
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