TAILIEUCHUNG - BWTaligner: a genome short-read aligner

The development of next-generation sequencing technologies has helped sequence large genomes easily, producing a huge number of short-reads - small fragments of DNA. Despite the existence of many developed alignment tools, mapping short-read datasets to the reference genome, a crucial step of genome analysis, still remains a challenge. In this study, we develop a short-read alignment program, BWTaligner, based on the Burrows-Wheeler transform compression - exact and inexact matching. We tested it on the paired-end read data simulated from chromosome 9 of the rice genome to compare the alignment and single-nucleotide polymorphism (SNP) calling between our aligner and BWA - the preferred alignment program. The results showed that the BWA delivers higher recall and F-score, while BWTaligner has better precision in high coverage depth. | LIFE SCIENCES BIOTECHNOLOGY BWTaligner a genome short-read aligner Lam Nguyen1 Xuan Thi Trinh2 Hien Trinh3 Dang Hung Tran4 Cuong Nguyen1 1Vinmec Research Institute of Stem Cell and Gene Technology 2Faculty of Information Technology Hanoi Open University 3Laboratory of Genetic Engineering Institute of Biotechnology Vietnam Academy of Science and Technology 4Hanoi National University of Education Received 6 April 2018 accepted 15 May 2018 Abstract The development of next-generation sequencing technologies has helped sequence large genomes easily producing a huge number of short-reads - small fragments of DNA. Despite the existence of many developed alignment tools mapping short-read datasets to the reference genome a crucial step of genome analysis still remains a challenge. In this study we develop a short-read alignment program BWTaligner based on the Burrows-Wheeler transform compression - exact and inexact matching. We tested it on the paired-end read data simulated from chromosome 9 of the rice genome to compare the alignment and single-nucleo-tide polymorphism SNP calling between our aligner and BWA - the preferred alignment program. The results showed that the BWA delivers higher recall and F-score while BWTaligner has better precision in high coverage depth. Keywords Burrows-Wheeler transform high-throughput sequencing paired-end short reads sequence alignment. Classification number Corresponding author Email vcuongn@ Introduction The development of massive parallel sequencing technologies has stimulated the production of a vast number of short-reads which are small fragments of DNA genomes. As the mapping of short-read datasets to large genomes presents a huge challenge to the existing sequencing programs more and more algorithms are being improved in order to reduce the execution time and increase the mapping accuracy. At the outset hash table-based methods either hash the short-read sequences or the reference genome and many alignment tools .

• Sinh học
• Genome short read aligner
• Burrows Wheeler transform
• High throughput sequencing
• Paired end short reads
• Sequence alignment
• Alignment kernel
• Dynamic programming
• Multiple sequence alignment
• Reference sequence alignment
• Distribution mechanisms
• Tree alignment
• Tree search
• Direct optimization
• Multiple sequence alignment problem
• BMC Bioinformatics
• Smith Waterman
• Pairwise sequence alignment
• Xeon Phi clusters
• Neuronal morphology
• Tree topology
• Secondary structure predictions
• Large scale alignment
• Benchmark datasets
• Modeling gap penalties
• Alignment graphs
• Statistical alignment
• Alignment uncertainty
• BMC Genomics
• Semi global alignment with traceback
• Optimal alignment
• Pairwise alignments
• Giải thuật nâng cao
• Bài giảng Giải thuật nâng cao
• Quy hoạch động
• Bài toán Sequence Alignment
• Dự án Human Genome
• Bài toán local sequence alignment
• Poisson process
• Dynamic homology
• Implied alignment
• Multiple string alignment
• International Journal of Computer Science and Telecommunications
• The grid computing using cache technique
• The previous alignment results
• The cache storage technique
• Center star alignment
• Biological datasets
• MSA parallelization
• Genome annotation
• Gene prediction
• Gene structure
• Spliced alignment
• Ribosomal proteins
• Sequence clustering
• Graphical manner
• Existing methods
• Homology based methods
• Sequence homology
• Bayesian statistics
• Alignment refinement
• Alignment improvement
• Secondary structure evaluation
• Protein sequence alignment
• A non contiguous Tree Sequence Alignment based Model
• Statistical Machine Translation
• Jun Sun
• báo cáo khoa học
• báo cáo ngôn ngữ
• xử lý ngôn ngữ tự nhiên
• A Tree Sequence Alignment based
• Tree to Tree Translation Model
• Min Zhang
• Parallel Implementation of MAFFT on CUDA Enabled
• CUDA Enabled Graphics Hardware
• Parallel Programming with CUDA
• Multiple Sequence Alignment and MAFFT Algorithm
• Previous Work of Sequence Alignment CUDA
• Profiling of MAFFT
• Tin sinh học đại cương
• Bài giảng Tin sinh học đại cương
• Bắt cặp trình tự
• Bắt cặp hai trình tự
• Bắt cặp nhiều trình tự
• Semantic web
• N tier architecture
• Microbial taxonomy ontology
• Agriculturally important microorganisms
• Sequence alignment reinforcement options
• Open source
• Color space
• Amino acids
• Contact prediction
• Convolutional neural network
• Deep learning
• Secondary structure prediction
• Indel flanking regions
• PPM IndelFR predictor
• Stochastic evolutionary model
• Probability distribution
• MSA space exploration