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Fast and accurate read alignment for resequencing

John C. Mu, Hui Jiang, Amirhossein Kiani, Marghoob Mohiyuddin, Narges Bani Asadi, Wing H. Wong
2012 Computer applications in the biosciences : CABIOS  
The accurate alignment of reads with large indels is a computationally challenging task for researchers. Results: We introduce SeqAlto as a new algorithm for read alignment.  ...  For reads longer than or equal to 100 bp, SeqAlto is up to 10 Â faster than existing algorithms, while retaining high accuracy and the ability to align reads with large (up to 50 bp) indels.  ...  In this article, we introduce SeqAlto, a fast and accurate read alignment tool that reliably align reads with large insertions and deletions (indels).  ... 
doi:10.1093/bioinformatics/bts450 pmid:22811546 pmcid:PMC3436849 fatcat:bqxq4tpnzvdadpakxdubxhl4sy

BFAST: An Alignment Tool for Large Scale Genome Resequencing

Nils Homer, Barry Merriman, Stanley F. Nelson, Chad Creighton
2009 PLoS ONE  
The new generation of massively parallel DNA sequencers, combined with the challenge of whole human genome resequencing, result in the need for rapid and accurate alignment of billions of short DNA sequence  ...  against read errors and sequence variants.  ...  Acknowledgments We would like to thank Jim Kent for creating and distributing the BLAT program, which was both a motivation for this work, and was also the basis for our practical large-scale alignment  ... 
doi:10.1371/journal.pone.0007767 pmid:19907642 pmcid:PMC2770639 fatcat:4oqad3kplfdstd4ujftpc7gvpq

Implementation and Data Analysis of Tn-seq, Whole-Genome Resequencing, and Single-Molecule Real-Time Sequencing for Bacterial Genetics

Peter E. Burby, Taylor M. Nye, Jeremy W. Schroeder, Lyle A. Simmons, W. Margolin
2016 Journal of Bacteriology  
for identification of suppressor or other mutations, and we summarize single-molecule real-time (SMRT) sequencing for de novo genome assembly and the use of the output data for detection of DNA base modifications  ...  We provide resources for scientists new to and interested in their application.  ...  While the method is highly accurate, fast, and relatively inexpensive, the Illumina platform yields short read lengths of between 50 and 300 bp, creating a major difficulty with respect to de novo genome  ... 
doi:10.1128/jb.00560-16 pmid:27672193 pmcid:PMC5165101 fatcat:6plc2efov5c63i7mm574zvtvdq

Genome-Wide SNP Calling from Genotyping by Sequencing (GBS) Data: A Comparison of Seven Pipelines and Two Sequencing Technologies

Davoud Torkamaneh, Jérôme Laroche, François Belzile, Hector Candela
2016 PLoS ONE  
It again called more polymorphisms (25.8K vs 22.9K) and these proved more accurate (95.2 vs 91.1%).  ...  Using Ion Torrent sequence data for the same 24 lines, we compared the performance of Fast-GBS with that of TASSEL-GBSv2.  ...  We selected Fast-GBS as the basis for comparison because of its ability to very accurately call a large number of SNPs.  ... 
doi:10.1371/journal.pone.0161333 pmid:27547936 pmcid:PMC4993469 fatcat:tokcy6m4ijcwhbqr45sjigwrxe

The need for speed

Paul Flicek
2009 Genome Biology  
The Bowtie sequence-alignment algorithm uses advanced data structures to help data analysis keep pace with data generation.  ...  The electronic version of this article is the complete one and can be found online at Genome B Bi io ol lo og gy y 2009, Volume 10, Issue 3, Article 212 Flicek 212.2 Genome B Bi io ol lo og gy y 2009,  ...  Bowtie is also currently missing some critical functionality (for example, the ability to align paired reads).  ... 
doi:10.1186/gb-2009-10-3-212 pmid:19344490 pmcid:PMC2690991 fatcat:2qvwlns2p5d67gscsm6prftvna

Fast-GBS: a new pipeline for the efficient and highly accurate calling of SNPs from genotyping-by-sequencing data

Davoud Torkamaneh, Jérôme Laroche, Maxime Bastien, Amina Abed, François Belzile
2017 BMC Bioinformatics  
Conclusions: We conclude that Fast-GBS provides a highly efficient and reliable tool for calling SNPs from GBS data.  ...  Herein we describe a new GBS bioinformatics pipeline, Fast-GBS, designed to provide highly accurate genotyping, to require modest computing resources and to offer ease of use.  ...  Funding Funding for this research was provided by Agriculture and AgriFood Canada and the Canadian Field Crop Research Alliance (Grant no. AIP-CL23).  ... 
doi:10.1186/s12859-016-1431-9 pmid:28049422 pmcid:PMC5210301 fatcat:fdpevldhfbfglgmo5nvulnhyz4

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

H. Li, J. Ruan, R. Durbin
2008 Genome Research  
Both read mapping and genotype calling are evaluated on simulated data and real data. MAQ is accurate, efficient, versatile, and user-friendly. It is freely available at  ...  MAQ makes full use of mate-pair information and estimates the error probability of each read alignment.  ...  We thank Julian Parkhill, Kathryn Holt, and the Sanger Institute pathogen sequencing unit for providing the S. paratyphi sequence, and the sequencing team and the sequencing informatics group for generating  ... 
doi:10.1101/gr.078212.108 pmid:18714091 pmcid:PMC2577856 fatcat:ewcxztyon5bcxidtiict7rpzga

Genomic variation and DNA repair associated with soybean transgenesis: a comparison to cultivars and mutagenized plants

Justin E. Anderson, Jean-Michel Michno, Thomas J. Y. Kono, Adrian O. Stec, Benjamin W. Campbell, Shaun J. Curtin, Robert M. Stupar
2016 BMC Biotechnology  
In this study, genomic structural variation (e.g. large deletions and duplications) and single nucleotide polymorphism rates were assessed among a sample of soybean cultivars, fast neutron-derived mutants  ...  Results: On average, the number of genes affected by structural variations in transgenic plants was one order of magnitude less than that of fast neutron mutants and two orders of magnitude less than the  ...  We are grateful to Carroll Vance and Gary Muehlbauer for contributing towards the resequencing of the FN plants.  ... 
doi:10.1186/s12896-016-0271-z pmid:27176220 pmcid:PMC4866027 fatcat:zih3gkqyvrfwbmghzdr2z5gqji

Fast Isogenic Mapping-by-Sequencing of Ethyl Methanesulfonate-Induced Mutant Bulks

B. Hartwig, G. V. James, K. Konrad, K. Schneeberger, F. Turck
2012 Plant Physiology  
Genetic analysis of two independent additional alleles confirmed that this mutation was causal for the suppression of lhp1.  ...  our mutant identification pipeline and thereby reduced the number of causal candidate mutations to only one.  ...  Resequencing Analysis We applied SHORE to independently align the read sets of the lhp1 mutant and the alp1-1;lhp1 double mutant to the Col-0 reference genome using GenomeMapper as an alignment tool (  ... 
doi:10.1104/pp.112.200311 pmid:22837357 pmcid:PMC3461541 fatcat:6dus2mooszf3figrevkehelkym

SeqHive: A Reconfigurable Computer Cluster for Genome Re-sequencing

Kristian Stevens, Henry Chen, Terry Filiba, Peter McMahon, Yun S. Song
2010 2010 International Conference on Field Programmable Logic and Applications  
A prerequisite to effectively utilizing this data for most applications is accurate alignment to a reference genome.  ...  Each FPGA is capable of rapidly aligning multiple reads in parallel against a long reference genome.  ...  Acknowledgments: We thank Venkatesh Akella, Dan Burke, Chen Chang, Charles Langley, Vinayak Nagpal, and John Wawrzynek for their input during this project.  ... 
doi:10.1109/fpl.2010.121 dblp:conf/fpl/StevensCFMS10 fatcat:ryjzreisnncuvjuioi75f7buti

Fast neutron mutagenesis in soybean enriches for small indels and creates frameshift mutations

Skylar R Wyant, M Fernanda Rodriguez, Corey K Carter, Wayne A Parrott, Scott A Jackson, Robert M Stupar, Peter L Morrell
2021 G3: Genes, Genomes, Genetics  
The mutagenic effects of ionizing radiation have been used for decades to create novel variants in experimental populations.  ...  , and translocations.  ...  Acknowledgments We thank members of the Morrell Lab for discussion and software testing.  ... 
doi:10.1093/g3journal/jkab431 pmid:35100358 fatcat:6tcwkqnem5ehphwxz7e2xysnfe

Searching for SNPs with cloud computing

Ben Langmead, Michael C Schatz, Jimmy Lin, Mihai Pop, Steven L Salzberg
2009 Genome Biology  
Crossbow is a cloud-computing software tool that combines the aligner Bowtie and the SNP caller SOAPsnp.  ...  As DNA sequencing outpaces improvements in computer speed, there is a critical need to accelerate tasks like alignment and SNP calling.  ...  We thank the Amazon Web Services Hadoop Testing Program for providing credits, and Deepak Singh for his assistance.  ... 
doi:10.1186/gb-2009-10-11-r134 pmid:19930550 pmcid:PMC3091327 fatcat:pppdfms72fe4lbfa25blly4l3i

RelocaTE2: a high resolution transposable element insertion site mapping tool for population resequencing

Jinfeng Chen, Travis R. Wrightsman, Susan R. Wessler, Jason E. Stajich
2017 PeerJ  
RelocaTE2 searches for known TE sequences in whole genome sequencing reads from second generation sequencing platforms such as Illumina.  ...  Methods We have developed the tool RelocaTE2 for identification of TE insertion sites at high sensitivity and specificity.  ...  This second category of tools is ideal for identifying new insertions from population resequencing data because it can accurately detect an insertion location along with the TSD.  ... 
doi:10.7717/peerj.2942 pmid:28149701 pmcid:PMC5274521 fatcat:35ht76hjpbdqxmqbwychyiw77q

Single-Molecule DNA Sequencing of a Viral Genome

T. D. Harris, P. R. Buzby, H. Babcock, E. Beer, J. Bowers, I. Braslavsky, M. Causey, J. Colonell, J. DiMeo, J. W. Efcavitch, E. Giladi, J. Gill (+11 others)
2008 Science  
The average and median read lengths were~23 bases for this run.  ...  This demonstrates a strategy for high-throughput low-cost resequencing.  ... 
doi:10.1126/science.1150427 pmid:18388294 fatcat:a6igzh7ejjfxzjqcthlpkzy7me

Altools: a user friendly NGS data analyser

Salvatore Camiolo, Gaurav Sablok, Andrea Porceddu
2016 Biology Direct  
Conclusions: Altools is fast, reliable and easy to use for the mining of NGS data.  ...  It also uses insert size information from the alignment of paired-end reads and detects potential large deletions.  ...  For this reason, the lead author would like to thank Prof. Andy  ... 
doi:10.1186/s13062-016-0110-0 pmid:26883204 pmcid:PMC4756442 fatcat:odpgnnegqjgblnrv3csuntkrxm
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