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ssahaSNP A Polymorphism Detection Tool on a Whole Genome Scale

Zemin Ning, M. Caccamo, J.C. Mullikin
2005 IEEE Computational Systems Bioinformatics Conference - Workshops (CSBW'05)  
We present a software package which can detect homozygous SNPs and indels on a eukaryotic genome scale from millions of shotgun reads.  ...  Matching seeds of a few kmer words are found to locate the position of the read on the genome. Full sequence alignment is performed to detect base variations.  ...  In the new version of ssahaSNP, we use ssaha2 as the alignment tool to place genomic reads on finished or draft assembly sequences.  ... 
doi:10.1109/csbw.2005.128 dblp:conf/csb/NingCM05 fatcat:fndxo7r7g5fd5fduhbafvayyvy

Next-generation sequencing technologies and their implications for crop genetics and breeding

Rajeev K. Varshney, Spurthi N. Nayak, Gregory D. May, Scott A. Jackson
2009 Trends in Biotechnology  
analysis/ssahaSNP/): tool to detect homozygous SNPs and indels.  ...  Molecular markers: a set of DNA-based markers that can detect DNA polymorphism at the level of specific loci and at the whole genome level.  ... 
doi:10.1016/j.tibtech.2009.05.006 pmid:19679362 fatcat:pqqn6vp5cvaavg4wzjjh7zh6tm

Computational SNP discovery in DNA sequence data

Gabor T Marth
2003 Msphere  
The development of a second generation of tools was prompted by the needs of genome-scale projects of SNP discovery.  ...  As a fast tool capable of efficient processing of large data sets, SSAHASNP was used in the discovery of a large fraction of SNPs in the TSC data (1).  ...  Run POLYPHRED on the multiple alignment to detect polymorphic sites. Using the "-ace" option, specify the "ACE" format PHRAP output file created in the previous step when invoking POLYPHRED.  ... 
pmid:12491905 fatcat:6u7q6tarx5cyxm5ghifojik5rq

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  
This tool is useful for analyzing sequence tagged sites (STSs) of genomic sequences, and this software can serve as a starting point for groups interested in developing SNP markers.  ...  This package was developed on UNIX/Linux platform, written in Perl and uses a MySQL database.  ...  of an optimal tool depends on the nature of input sequences.  ... 
doi:10.1186/1471-2105-7-468 pmid:17059604 pmcid:PMC1626092 fatcat:zyafmdtcgjbybka7lpk2qaujma

High-Throughput Detection of Induced Mutations and Natural Variation Using KeyPoint™ Technology

Diana Rigola, Jan van Oeveren, Antoine Janssen, Anita Bonné, Harrie Schneiders, Hein J. A. van der Poel, Nathalie J. van Orsouw, René C. J. Hogers, Michiel T. J. de Both, Michiel J. T. van Eijk, Alfredo Herrera-Estrella
2009 PLoS ONE  
We present KeyPoint TM technology, a high-throughput mutation/polymorphism discovery technique based on massive parallel sequencing of target genes amplified from mutant or natural populations.  ...  Reverse genetics approaches rely on the detection of sequence alterations in target genes to identify allelic variants among mutant or natural populations.  ...  Contributed reagents/materials/analysis tools: JvO AJ. Wrote the paper: DR MJTvE.  ... 
doi:10.1371/journal.pone.0004761 pmid:19283079 pmcid:PMC2654077 fatcat:tnenft2mkzdpni4boig4hwyq4q

Utilization of next-generation sequencing platforms in plant genomics and genetic variant discovery

Stéphane Deschamps, Matthew A. Campbell
2009 Molecular breeding  
Genome-wide variant detection within a species is the primary initial step towards linking genotypic variation and phenotypes.  ...  far more comprehensive view of the genome or transcriptome.  ...  The ssahaSNP ( analysis/ssahaSNP) alignment tool detects homozygous SNPS and indels after aligning short reads to a reference genome.  ... 
doi:10.1007/s11032-009-9357-9 fatcat:h6tjrzh7bbbrffxgl4hza23h7m

Mapping and sequencing of structural variation from eight human genomes

Jeffrey M. Kidd, Gregory M. Cooper, William F. Donahue, Hillary S. Hayden, Nick Sampas, Tina Graves, Nancy Hansen, Brian Teague, Can Alkan, Francesca Antonacci, Eric Haugen, Troy Zerr (+34 others)
2008 Nature  
Here we explore variation on an intermediate scale-particularly insertions, deletions and inversions affecting from a few thousand to a few million base pairs.  ...  Genetic variation among individual humans occurs on many different scales, ranging from gross alterations in the human karyotype to single nucleotide changes.  ...  Acknowledgements We thank the staff from the University of Washington Genome Center and the Washington University Genome Sequencing Center for technical assistance.  ... 
doi:10.1038/nature06862 pmid:18451855 pmcid:PMC2424287 fatcat:omkkwzhdezdehnqzauhg2udcem

Transcriptome Analysis of the Mud Crab (Scylla paramamosain) by 454 Deep Sequencing: Assembly, Annotation, and Marker Discovery

Hongyu Ma, Chunyan Ma, Shujuan Li, Wei Jiang, Xincang Li, Yuexing Liu, Lingbo Ma, Cynthia Gibas
2014 PLoS ONE  
In addition, 19,011 microsatellites and 37,063 potential single nucleotide polymorphisms were detected from the transcriptome of S. paramamosain.  ...  A total of 1,314,101 high quality reads with an average length of 411 bp were generated by 454 sequencing on a mixed cDNA library.  ...  To our knowledge, neither whole genome sequencing project, nor large-scale next-generation sequencing research of S. paramamosain was reported to date.  ... 
doi:10.1371/journal.pone.0102668 pmid:25054331 pmcid:PMC4108364 fatcat:zpxpmdmxr5h4hm3bsstyvchqru

Mapping short DNA sequencing reads and calling variants using mapping quality scores

H. Li, J. Ruan, R. Durbin
2008 Genome Research  
We describe the software MAQ that can build assemblies by mapping shotgun short reads to a reference genome, using quality scores to derive genotype calls of the consensus sequence of a diploid genome,  ...  In particular, there is a major issue in efficiently aligning short reads to a reference genome and handling ambiguity or lack of accuracy in this alignment.  ...  Acknowledgments We thank Tony Cox, Keira Cheetham, Richard Carter, and David Bentley from Illumina for beneficial discussions on consensus genotype calling.  ... 
doi:10.1101/gr.078212.108 pmid:18714091 pmcid:PMC2577856 fatcat:ewcxztyon5bcxidtiict7rpzga

Allele Identification in Assembled Genomic Sequence Datasets [chapter]

Katrina M. Dlugosch, Aurélie Bonin
2012 Msphere  
Our focus is particularly on the case where alleles must be identi fi ed without a fully resolved reference genome, and where sequence depth information cannot be used to infer the putative number of loci  ...  Throughout, we provide information about publicly available tools to aid allele identi fi cation in such cases.  ...  Acknowledgments We thank MS Barker, LH Rieseberg, I Mayrose, and SP Otto for insightful discussions on this topic.  ... 
doi:10.1007/978-1-61779-870-2_12 pmid:22665283 fatcat:xvevhceeijaaff3424cldvtrum

Transcriptome analysis of the differences in gene expression between testis and ovary in green mud crab (Scylla paramamosain)

Jie Gao, Xiaowei Wang, Zhihua Zou, Xiwei Jia, Yilei Wang, Ziping Zhang
2014 BMC Genomics  
A large number of candidate SSRs and SNPs were detected, which could be used as genetic markers for population genetics and functional genomics in this species.  ...  The green mud crab (Scylla paramamosain) is the most prevalent crustacean on the southeast coast of China.  ...  It is expected that these SSRs and SNPs will play a tremendous role in the exploration and utilization of new genes S. paramamosain, and will be developed as a tool for genomics and functional genomics  ... 
doi:10.1186/1471-2164-15-585 pmid:25015001 pmcid:PMC4124137 fatcat:yukww3qeknfblm7z7gmvdlwfpa

Single-Nucleotide Polymorphism Bioinformatics: A Comprehensive Review of Resources

A. D. Johnson
2009 Circulation: Cardiovascular Genetics  
The PLINK whole genome association toolkit also includes a module for correction based on identical by state calculations for whole genome genotyping data. 27 Another approach often applied in whole  ...  the genome-wide scale.  ... 
doi:10.1161/circgenetics.109.872010 pmid:20031630 pmcid:PMC2789466 fatcat:hpihw32xhjbapibxxvggljvnum

High-throughput genotyping by whole-genome resequencing

X. Huang, Q. Feng, Q. Qian, Q. Zhao, L. Wang, A. Wang, J. Guan, D. Fan, Q. Weng, T. Huang, G. Dong, T. Sang (+1 others)
2009 Genome Research  
With continuous advances in sequencing technologies, this genome-based method may replace the conventional marker-based genotyping approach to provide a powerful tool for large-scale gene discovery and  ...  We have developed a high-throughput method for genotyping recombinant populations utilizing whole-genome resequencing data generated by the Illumina Genome Analyzer.  ...  thank Zemin Ning for assistance with sequence alignment, Chuanrang Zhu and Tingting Lu for computational assistance and helpful discussion, and Qifa Zhang and anonymous reviewers for valuable comments on  ... 
doi:10.1101/gr.089516.108 pmid:19420380 pmcid:PMC2694477 fatcat:enqw4gqkvrh4tlddphhfx2klzu

Transcriptomic Analysis ofEucryptorrhynchus chinensis(Coleoptera: Curculionidae) Using 454 Pyrosequencing Technology

Zhen-Kai Liu, Jun-Bao Wen
2016 Journal of Insect Science  
A total of 659,026 single nucleotide variants and 6,112 simple sequence repeats were detected.  ...  Eucryptorrhynchus chinensis Olivier (Coleoptera: Curculionidae) is one of the most important pests of Ailanthus altissima; however, so far, no studies on the genome or transcriptome of E. chinensis have  ...  SSR markers (Thiel et al. 2003) . ssahaSNP software was used to detect SNVs and indels in the assembled isotigs (van Oeveren and Janssen 2009).  ... 
doi:10.1093/jisesa/iew067 pmid:27620556 pmcid:PMC5019023 fatcat:3dtc2sge4nftzi55rwuu3wzcoe

SNP detection for massively parallel whole-genome resequencing

R. Li, Y. Li, X. Fang, H. Yang, J. Wang, K. Kristiansen, J. Wang
2009 Genome Research  
One of the key applications of next-generation sequencing is studying genetic variation between individuals using whole-genome or target region resequencing.  ...  Here, we have developed a consensus-calling and SNP-detection method for sequencing-by-synthesis Illumina Genome Analyzer technology.  ...  With high-throughput clone sequencing of shotgun libraries, a standard method for SNP detection (such as ssahaSNP; Ning et al. 2001) is to align the reads onto a reference genome and filter low-quality  ... 
doi:10.1101/gr.088013.108 pmid:19420381 pmcid:PMC2694485 fatcat:c3wlnwtm2jhz7biizey43tks54
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