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Improving SNP discovery by base alignment quality
2011
Bioinformatics
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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
2006
BMC Bioinformatics
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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
2012
PLoS ONE
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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
2006
BMC Bioinformatics
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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
2008
Nature Methods
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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
2013
Scientific Reports
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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
2011
BMC Genomics
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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
2013
PLoS ONE
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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
2010
Genome Biology
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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
2013
PLoS ONE
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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
2010
Computer applications in the biosciences : CABIOS
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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
2019
BMC Genomics
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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
2009
BMC Genomics
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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
2010
BMC Genomics
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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
2011
Genome Biology
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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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