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https://www.readbyqxmd.com/read/29114401/aligner-optimization-increases-accuracy-and-decreases-compute-times-in-multi-species-sequence-data
#1
Kelly M Robinson, Aziah S Hawkins, Ivette Santana-Cruz, Ricky S Adkins, Amol C Shetty, Sushma Nagaraj, Lisa Sadzewicz, Luke J Tallon, David A Rasko, Claire M Fraser, Anup Mahurkar, Joana C Silva, Julie C Dunning Hotopp
As sequencing technologies have evolved, the tools to analyze these sequences have made similar advances. However, for multi-species samples, we observed important and adverse differences in alignment specificity and computation time for bwa- mem (Burrows-Wheeler aligner-maximum exact matches) relative to bwa-aln. Therefore, we sought to optimize bwa-mem for alignment of data from multi-species samples in order to reduce alignment time and increase the specificity of alignments. In the multi-species cases examined, there was one majority member (i...
September 2017: Microbial Genomics
https://www.readbyqxmd.com/read/29106455/virapipe-scalable-parallel-pipeline-for-viral-metagenome-analysis-from-next-generation-sequencing-reads
#2
Altti Ilari Maarala, Zurab Bzhalava, Joakim Dillner, Keijo Heljanko, Davit Bzhalava
Motivation: Next Generation Sequencing (NGS) technology enables identification of microbial genomes from massive amount of human microbiomes more rapidly and cheaper than ever before. However, the traditional sequential genome analysis algorithms, tools, and platforms are inefficient for performing large-scale metagenomic studies on ever-growing sample data volumes. Currently, there is an urgent need for scalable analysis pipelines that enable harnessing all the power of parallel computation in computing clusters and in cloud computing environments...
November 2, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29080873/-a-bioinformatic-pipeline-for-ngs-data-analysis-and-mutation-calling-in-human-solid-tumors
#3
K Yu Tsukanov, A Yu Krasnenko, D A Plakhina, D O Korostin, A V Churov, O S Druzhilovskaya, D V Rebrikov, V V Ilinsky
We aimed to develop a pipeline for the bioinformatic analysis and interpretation of NGS data and detection of a wide range of single-nucleotide somatic mutations within tumor DNA. Initially, the NGS reads were submitted to a quality control check by the Cutadapt program. Low-quality 3¢-nucleotides were removed. After that the reads were mapped to the reference genome hg19 (GRCh37.p13) by BWA. The SAMtools program was used for exclusion of duplicates. MuTect was used for SNV calling. The functional effect of SNVs was evaluated using the algorithm, including annotation and evaluation of SNV pathogenicity by SnpEff and analysis of such databases as COSMIC, dbNSFP, Clinvar, and OMIM...
October 2017: Biomedit︠s︡inskai︠a︡ Khimii︠a︡
https://www.readbyqxmd.com/read/28961906/crispr-dav-crispr-ngs-data-analysis-and-visualization-pipeline
#4
Xuning Wang, Charles Tilford, Isaac Neuhaus, Gabe Mintier, Qi Guo, John N Feder, Stefan Kirov
Summary: The simplicity and precision of CRISPR/Cas9 system has brought in a new era of gene editing. Screening for desired clones with CRISPR-mediated genomic edits in a large number of samples is made possible by next generation sequencing (NGS) due to its multiplexing. Here we present CRISPR-DAV (CRISPR Data Analysis and Visualization) pipeline to analyze the CRISPR NGS data in a high throughput manner. In the pipeline, BWA and ABRA are used for small and large indel detection, and results are presented in a comprehensive set of charts and interactive alignment view...
August 14, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28938228/sex-determination-from-chest-measurements-in-a-sample-of-egyptian-adults-using-multislice-computed-tomography
#5
Ragaa T Darwish, Manal H Abdel-Aziz, Abdel-Aziz M El Nekiedy, Zahraa K Sobh
BACKGROUND: In forensic sciences to determine one's sex is quite important during the identity defining stage. The reliability of sex determination depends on the completeness of the remains and the degree of sexual dimorphism inherent in the population. Computed Tomography is the imaging modality of choice for two- and three-dimensional documentation and analysis of many autopsy findings. OBJECTIVE: The aim of the present work was to assess the reliability of Three-dimensional Multislice Computed Tomography (3D MSCT) to determine sexual dimorphism from certain chest measurements; sternum and fourth rib using the 3D MSCT and to develop equations for sex determination from these bones among adult Egyptians sample...
September 11, 2017: Journal of Forensic and Legal Medicine
https://www.readbyqxmd.com/read/28912480/genome-wide-rad-sequencing-data-provide-unprecedented-resolution-of-the-phylogeny-of-temperate-bamboos-poaceae-bambusoideae
#6
Xueqin Wang, Xiaying Ye, Lei Zhao, Dezhu Li, Zhenhua Guo, Huifu Zhuang
The temperate bamboos (tribe Arundinarieae, Poaceae) are strongly supported as monophyly in recent molecular studies, but taxonomic delineation and phylogenetic relationships within the tribe lack resolution. Here, we sampled 39 species (36 temperate bamboos and 3 outgroups) for restriction-site associated DNA sequencing (RAD-seq) with an emphasis on Phyllostachys clade and related clades. Using the largest data matrix for the bamboos to date, we were able to infer phylogenetic relationships with unparalleled resolution...
September 14, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28854595/dormancy-and-activation-of-human-oocytes-from-primordial-and-primary-follicles-molecular-clues-to-oocyte-regulation
#7
E H Ernst, M L Grøndahl, S Grund, K Hardy, A Heuck, L Sunde, S Franks, C Y Andersen, P Villesen, K Lykke-Hartmann
STUDY QUESTION: Do specific transcriptome dynamics in human oocytes from primordial and primary follicles identify novel pathways in oocyte activation? SUMMARY ANSWER: The transcriptomic profiles in oocytes from primordial and primary follicles, respectively, revealed several new canonical pathways as putative mediators of oocyte dormancy and activation. WHAT IS KNOWN ALREADY: Cellular signaling pathways including PI3K/AKT and AKT/mTOR as well as TGF-β and IGF signaling are known to regulate the primordial-to-primary transition in mammalian follicle development...
August 1, 2017: Human Reproduction
https://www.readbyqxmd.com/read/28623477/use-of-the-boadicea-web-application-in-clinical-practice-appraisals-by-clinicians-from-various-countries
#8
Anne Brédart, Jean-Luc Kop, Antonis C Antoniou, Alex P Cunningham, Antoine De Pauw, Marc Tischkowitz, Hans Ehrencrona, Sylvie Dolbeault, Léonore Robieux, Kerstin Rhiem, Douglas F Easton, Peter Devilee, Dominique Stoppa-Lyonnet, Rita Schmutlzer
The 'BOADICEA' Web Application (BWA) used to assess breast cancer risk, is currently being further developed, to integrate additional genetic and non-genetic factors. We surveyed clinicians' perceived acceptability of the existing BWA v3. An online survey was conducted through the BOADICEA website, and the British, Dutch, French and Swedish genetics societies. Cross-sectional data from 443 participants who provided at least 50% responses were analysed. Respondents varied in age and, clinical seniority, but mainly comprised women (77%) and genetics professionals (82%)...
June 16, 2017: Familial Cancer
https://www.readbyqxmd.com/read/28531267/alignment-of-1000-genomes-project-reads-to-reference-assembly-grch38
#9
Xiangqun Zheng-Bradley, Ian Streeter, Susan Fairley, David Richardson, Laura Clarke, Paul Flicek
The 1000 Genomes Project produced more than 100 trillion basepairs of short read sequence from more than 2600 samples in 26 populations over a period of five years. In its final phase, the project released over 85 million genotyped and phased variants on human reference genome assembly GRCh37. An updated reference assembly, GRCh38, was released in late 2013, but there was insufficient time for the final phase of the project analysis to change to the new assembly. Although it is possible to lift the coordinates of the 1000 Genomes Project variants to the new assembly, this is a potentially error-prone process as coordinate remapping is most appropriate only for non-repetitive regions of the genome and those that did not see significant change between the two assemblies...
July 1, 2017: GigaScience
https://www.readbyqxmd.com/read/28475232/safety-and-efficacy-of-sofosbuvir-based-direct-acting-antiviral-regimens-for-hepatitis-c-virus-genotypes-1-4-and-6-in-myanmar-real-world-experience
#10
N K T Hlaing, R A Mitrani, S T Aung, W W Phyo, M Serper, A M M Kyaw, A H Bwa, K M Win, K R Reddy
This open-label, clinical experience investigated the safety and efficacy of direct-acting antiviral (DAA) hepatitis C virus (HCV) therapy in Myanmar; 344 patients completed treatment between June 2015 and May 2016. Patients with HCV genotypes 1-4 and 6 received one of four treatments: (i) Peg-interferon (PEG-IFN)+sofosbuvir (SOF)+ribavirin (RBV) for 12 weeks, (ii) SOF+RBV for 24 weeks, (iii) ledipasvir (LDV)+SOF for 12 weeks or (iv) daclatasvir (DCV)+SOF+RBV for 12 or 24 weeks. Genotype 3 was most common (n=133, 38...
November 2017: Journal of Viral Hepatitis
https://www.readbyqxmd.com/read/28407084/comparative-analysis-of-de-novo-assemblers-for-variation-discovery-in-personal-genomes
#11
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
#12
COMPARATIVE STUDY
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...
July 2017: Genomics
https://www.readbyqxmd.com/read/28249565/statistical-method-to-compare-massive-parallel-sequencing-pipelines
#13
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
#14
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
#15
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
#16
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
#17
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
#18
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
#19
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
#20
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
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