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Improving SNP discovery by base alignment quality

H. Li
2011 Bioinformatics  
The central concept is per-Base Alignment Quality, which accurately measures the probability of a read base being wrongly aligned.  ...  I propose a new application of profile Hidden Markov Models in the area of SNP discovery from resequencing data, to greatly reduce false SNP calls caused by misalignments around insertions and deletions  ...  Marth and Hyun Min Kang whose works have inspired me to develop BAQ, to the 1000 Genomes Project analysis subgroup for the helpful discussions and to the three reviewers whose comments have helped me to improve  ... 
doi:10.1093/bioinformatics/btr076 pmid:21320865 pmcid:PMC3072548 fatcat:dlzeoswr7nfbtn44mw772llfie

SNP-PHAGE--High throughput SNP discovery pipeline

Lakshmi K Matukumalli, John J Grefenstette, David L Hyten, Ik-Young Choi, Perry B Cregan, Curtis P Van Tassell
2006 BMC Bioinformatics  
Although these tasks are routinely performed by several groups, an integrated open source SNP discovery pipeline that can be easily adapted by new groups interested in SNP marker development is currently  ...  A machine learning tool developed by this group for increasing the efficiency of SNP discovery is integrated as a part of this package as an optional feature.  ...  Acknowledgements The authors would like to thank all anonymous reviewers for their insightful comments and helpful suggestions in greatly improving the quality of manuscript presentation.  ... 
doi:10.1186/1471-2105-7-468 pmid:17059604 pmcid:PMC1626092 fatcat:zyafmdtcgjbybka7lpk2qaujma

Customisation of the Exome Data Analysis Pipeline Using a Combinatorial Approach

Swetansu Pattnaik, Srividya Vaidyanathan, Durgad G. Pooja, Sa Deepak, Binay Panda, Paolo Provero
2012 PLoS ONE  
To this end, we have sampled different freely available tools used at the alignment and post alignment stage suggesting the use of the most suitable combination determined by a simple framework of pre-existing  ...  Customarily, a consensus approach is used to overcome the systematic errors inherent to the sequencing technology, alignment and post alignment variant detection algorithms.  ...  We have recorded useful insights centred around time associated with read alignment, quality of alignment and variant calling based on their quality scores and variant re-discovery rates from genotyping  ... 
doi:10.1371/journal.pone.0030080 pmid:22238694 pmcid:PMC3253117 fatcat:m3awmc47jvb5noea52qr2pfn44

Application of machine learning in SNP discovery

Lakshmi K Matukumalli, John J Grefenstette, David L Hyten, Ik-Young Choi, Perry B Cregan, Curtis P Van Tassell
2006 BMC Bioinformatics  
ML support software is written in Perl and can be easily integrated into an existing SNP discovery pipeline.  ...  Test data of 18,390 candidate SNP were generated similarly from 1359 additional STS (8 Mb). SNP from both sets were classified by experts.  ...  Acknowledgements The authors like to thank Raymond Fernalld in validating SNP as a subject matter expert.  ... 
doi:10.1186/1471-2105-7-4 pmid:16398931 pmcid:PMC1955739 fatcat:jgmd5nbxbbc2lbqpul76frm7c4

Pyrobayes: an improved base caller for SNP discovery in pyrosequences

Aaron R Quinlan, Donald A Stewart, Michael P Strömberg, Gábor T Marth
2008 Nature Methods  
Concordance of base errors in the Pyrobayes and the native 454 base calls. Supplementary Figure 4. Distribution of base quality scores within homopolymer runs. Supplementary Figure 5.  ...  Base quality accuracy for the 454 Life Sciences FLX model. Supplementary Methods SUPPLEMENTARY FIGURE 1. The PYROBAYES base calling approach. Supplementary Figure 1.  ...  We then used the POLYBAYES SNP discovery program 12 to call SNP candidates among the aligned sequences from each base caller.  ... 
doi:10.1038/nmeth.1172 pmid:18193056 fatcat:dmxyelmjozdtlab7xmxin3ftyi

Using False Discovery Rates to Benchmark SNP-callers in next-generation sequencing projects

Rhys A. Farrer, Daniel A. Henk, Dan MacLean, David J. Studholme, Matthew C. Fisher
2013 Scientific Reports  
2013) Using false discovery rates to benchmark SNP-callers in next-generation sequencing projects. Scientific Reports, 3.  ...  In addition to this tool for comparing False Discovery Rates (FDR), we include a method for determining homozygous and heterozygous positions from an alignment using binomial probabilities for an expected  ...  Pre-processing reads prior to alignment by removing low quality reads or 39 ends is a common initial step to improve alignment accuracy.  ... 
doi:10.1038/srep01512 pmid:23518929 pmcid:PMC3604800 fatcat:3hiyjye5nfd45az4c6s7a2n7wa

Whole genome sequencing of peach (Prunus persica L.) for SNP identification and selection

Riaz Ahmad, Dan E Parfitt, Joseph Fass, Ebenezer Ogundiwin, Amit Dhingra, Thomas M Gradziel, Dawei Lin, Nikhil A Joshi, Pedro J Martinez-Garcia, Carlos H Crisosto
2011 BMC Genomics  
This improved sequencing capacity can now be used to do genome-wide SNP discovery for non-model organisms [9] [10] [11] [12] . Three parents, 'Dr.  ...  [24] suggested that longer single reads are better for SNP discovery.  ... 
doi:10.1186/1471-2164-12-569 pmid:22108025 pmcid:PMC3253712 fatcat:iebye4kqifetblrude4khsoppq

SNP Discovery in European Anchovy (Engraulis encrasicolus, L) by High-Throughput Transcriptome and Genome Sequencing

Iratxe Montes, Darrell Conklin, Aitor Albaina, Simon Creer, Gary R. Carvalho, María Santos, Andone Estonba, Yi-Hsiang Hsu
2013 PLoS ONE  
A novel method for detecting potential intron-exon boundaries in areas of putative SNPs has also been applied in silico to improve genotyping success.  ...  In all, 2,317 filtered putative transcriptome SNPs suitable for genotyping primer design were identified.  ...  Further support provided by colleagues from the Molecular Ecology and Fisheries Genetics Laboratory (MEFGL) in Bangor and from Pablo Markaide in University of the Basque Country (UPV/EHU) is gratefully  ... 
doi:10.1371/journal.pone.0070051 pmid:23936375 pmcid:PMC3731364 fatcat:eworakzvkngjfg5uqmd2w3drlq

Improved variant discovery through local re-alignment of short-read next-generation sequencing data using SRMA

Nils Homer, Stanley F Nelson
2010 Genome Biology  
A primary component of next-generation sequencing analysis is to align short reads to a reference genome, with each read aligned independently.  ...  Abstract A primary component of next-generation sequencing analysis is to align short reads to a reference genome, with each read aligned independently.  ...  Acknowledgements This research was supported by the NIH Neuroscience Microarray Consortium (U24NS052108) as well as grants from the NIMH (R01 MH071852), and NHGRI (U01HG005210).  ... 
doi:10.1186/gb-2010-11-10-r99 pmid:20932289 pmcid:PMC3218665 fatcat:hfpr3zm4orhfnlftny7f2ggkoy

Genotyping by Genome Reducing and Sequencing for Outbred Animals

Qiang Chen, Yufang Ma, Yumei Yang, Zhenliang Chen, Rongrong Liao, Xiaoxian Xie, Zhen Wang, Pengfei He, Yingying Tu, Xiangzhe Zhang, Changsuo Yang, Hongjie Yang (+6 others)
2013 PLoS ONE  
Here, we reported a new method for SNP genotyping, called genotyping by genome reducing and sequencing (GGRS) to genotype outbred species.  ...  Through an improved procedure for library preparation and a marker discovery and genotyping pipeline, the GGRS approach can genotype outbred species cost-effectively and high-reproducibly.  ...  The higher quality score and longer sequence per reads have advantages of true SNP discovery by validly mapping to reference genome sequence, which was crucial for accurate genotyping by directly sequencing  ... 
doi:10.1371/journal.pone.0067500 pmid:23874423 pmcid:PMC3715491 fatcat:r7ecosvjyndyxedulcoalwopkq

ACCUSA—accurate SNP calling on draft genomes

Sebastian Fröhler, Christoph Dieterich
2010 Computer applications in the biosciences : CABIOS  
To our knowledge, none of the existing single nucleotide polymorphism (SNP) callers consider the quality of the reference genome, which is not necessary for highquality assemblies of well-studied model  ...  However, most genome projects will remain in draft status with little to no genome assembly improvement due to time and financial constraints.  ...  SNP discovery approaches usually screen a set of candidate regions by analyzing multiple nucleotide alignments.  ... 
doi:10.1093/bioinformatics/btq138 pmid:20363730 fatcat:4iijxyjklneadageog5xyacq34

Benchmarking variant identification tools for plant diversity discovery

Xing Wu, Christopher Heffelfinger, Hongyu Zhao, Stephen L. Dellaporta
2019 BMC Genomics  
A 2-step imputation method, which utilized a set of high-confidence SNPs as the reference panel, showed up to 60% higher accuracy than direct LD-based imputation.  ...  This study serves as an important guiding information for plant biologists utilizing next-generation sequencing data for diversity characterization and crop improvement.  ...  This project has been supported by the National Science Foundation Plant Genome Research Program to SLD (#1444478).  ... 
doi:10.1186/s12864-019-6057-7 pmid:31500583 pmcid:PMC6734213 fatcat:ixmprlcu4nakxadlynmzpwjzxu

Large scale single nucleotide polymorphism discovery in unsequenced genomes using second generation high throughput sequencing technology: applied to turkey

Hindrik HD Kerstens, Richard PMA Crooijmans, Albertine Veenendaal, Bert W Dibbits, Thomas FC Chin-A-Woeng, Johan T den Dunnen, Martien AM Groenen
2009 BMC Genomics  
For the high throughput discovery of single nucleotide polymorphisms (SNPs) in species lacking a sequenced reference genome, we set-up an analysis pipeline based on a short read de novo sequence assembler  ...  Increasing the reference genome by adding publicly available turkey BAC-end sequences increased the number of SNPs to over 11,000.  ...  This study was funded by European Union grant FOOD-CT-2004-506416 (Eadgene), Netherlands National Computing Facilities foundation grant SH-018-07, and Hendrix Genetics, the Netherlands.  ... 
doi:10.1186/1471-2164-10-479 pmid:19835600 pmcid:PMC2772860 fatcat:2fnht7p2azerln7kfcj2b33joe

SNP discovery by high-throughput sequencing in soybean

Xiaolei Wu, Chengwei Ren, Trupti Joshi, Tri Vuong, Dong Xu, Henry T Nguyen
2010 BMC Genomics  
This SNP discovery approach is more efficient for targeting multiple QTL regions in a same genetic population, which can be applied to other crops.  ...  Results: A total of 39,022 putative SNPs were identified by the Illumina/Solexa sequencing system using a reduced representation DNA library of two parental lines of a mapping population.  ...  Acknowledgements This project was supported by the National Center for Soybean Biotechnology, and the Missouri Soybean Merchandising Council. The authors gratefully acknowledge Sean Blake, Curtis P.  ... 
doi:10.1186/1471-2164-11-469 pmid:20701770 pmcid:PMC3091665 fatcat:ibn5simyxnbwxgjw2nfr2xpxvq

Sniper: improved SNP discovery by multiply mapping deep sequenced reads

Daniel F Simola, Junhyong Kim
2011 Genome Biology  
SNP (single nucleotide polymorphism) discovery using next-generation sequencing data remains difficult primarily because of redundant genomic regions, such as interspersed repetitive elements and paralogous  ...  Our model fully accounts for sequencing error, template bias, and multi-locus SNP combinations, maintaining high sensitivity and specificity under a broad range of conditions.  ...  This work was supported by a HRFF grant to University of Pennsylvania from the Pennsylvania Common Wealth and by the Penn Genome Frontiers Institute and a grant with the Pennsylvania Department of Health  ... 
doi:10.1186/gb-2011-12-6-r55 pmid:21689413 pmcid:PMC3218843 fatcat:oopo6xivhrfyjkgy7e6r7i3k24
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