Next-Generation Sequence Assembly: Four Stages of Data Processing and Computational Challenges
出版年份 2013 全文链接
标题
Next-Generation Sequence Assembly: Four Stages of Data Processing and Computational Challenges
作者
关键词
-
出版物
PLoS Computational Biology
Volume 9, Issue 12, Pages e1003345
出版商
Public Library of Science (PLoS)
发表日期
2013-12-13
DOI
10.1371/journal.pcbi.1003345
参考文献
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注意:仅列出部分参考文献,下载原文获取全部文献信息。- Sequence assembly demystified
- (2013) Niranjan Nagarajan et al. NATURE REVIEWS GENETICS
- Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species
- (2013) Keith R Bradnam et al. GigaScience
- VAGUE: a graphical user interface for the Velvet assembler
- (2012) D. R. Powell et al. BIOINFORMATICS
- Exploring single-sample SNP and INDEL calling with whole-genome de novo assembly
- (2012) H. Li BIOINFORMATICS
- SCARPA: scaffolding reads with practical algorithms
- (2012) N. Donmez et al. BIOINFORMATICS
- Slim-Filter: an interactive windows-based application for illumina genome analyzer data assessment and manipulation
- (2012) Georgiy Golovko et al. BMC BIOINFORMATICS
- Readjoiner: a fast and memory efficient string graph-based sequence assembler
- (2012) Giorgio Gonnella et al. BMC BIOINFORMATICS
- Exploiting sparseness in de novo genome assembly
- (2012) Chengxi Ye et al. BMC BIOINFORMATICS
- A tale of three next generation sequencing platforms: comparison of Ion torrent, pacific biosciences and illumina MiSeq sequencers
- (2012) Michael Quail et al. BMC GENOMICS
- Optimizing hybrid assembly of next-generation sequence data from Enterococcus faecium: a microbe with highly divergent genome
- (2012) Yajun Wang et al. BMC Systems Biology
- A survey of error-correction methods for next-generation sequencing
- (2012) X. Yang et al. BRIEFINGS IN BIOINFORMATICS
- Mass spectrum sequential subtraction speeds up searching large peptide MS/MS spectra datasets against large nucleotide databases for proteogenomics
- (2012) Mohamed Helmy et al. GENES TO CELLS
- Performance comparison of benchtop high-throughput sequencing platforms
- (2012) Nicholas J Loman et al. NATURE BIOTECHNOLOGY
- NGS analyses by visualization with Trackster
- (2012) Jeremy Goecks et al. NATURE BIOTECHNOLOGY
- Hybrid error correction and de novo assembly of single-molecule sequencing reads
- (2012) Sergey Koren et al. NATURE BIOTECHNOLOGY
- Feature-by-Feature – Evaluating De Novo Sequence Assembly
- (2012) Francesco Vezzi et al. PLoS One
- Quake: quality-aware detection and correction of sequencing errors
- (2012) David R Kelley et al. GENOME BIOLOGY
- Landscape of Next-Generation Sequencing Technologies
- (2011) Thomas P. Niedringhaus et al. ANALYTICAL CHEMISTRY
- Comparative studies of de novo assembly tools for next-generation sequencing technologies
- (2011) Yong Lin et al. BIOINFORMATICS
- Succinct data structures for assembling large genomes
- (2011) Thomas C. Conway et al. BIOINFORMATICS
- Correcting errors in short reads by multiple alignments
- (2011) L. Salmela et al. BIOINFORMATICS
- Error correction of high-throughput sequencing datasets with non-uniform coverage
- (2011) P. Medvedev et al. BIOINFORMATICS
- Fast scaffolding with small independent mixed integer programs
- (2011) L. Salmela et al. BIOINFORMATICS
- Bambus 2: scaffolding metagenomes
- (2011) Sergey Koren et al. BIOINFORMATICS
- Efficient counting of k-mers in DNA sequences using a bloom filter
- (2011) Páll Melsted et al. BMC BIOINFORMATICS
- Evaluation of short read metagenomic assembly
- (2011) Anveshi Charuvaka et al. BMC GENOMICS
- Comparison of the two major classes of assembly algorithms: overlap-layout-consensus and de-bruijn-graph
- (2011) Z. Li et al. Briefings in Functional Genomics
- Assemblathon 1: A competitive assessment of de novo short read assembly methods
- (2011) D. Earl et al. GENOME RESEARCH
- ECHO: A reference-free short-read error correction algorithm
- (2011) W.-C. Kao et al. GENOME RESEARCH
- Efficient de novo assembly of large genomes using compressed data structures
- (2011) J. T. Simpson et al. GENOME RESEARCH
- GAGE: A critical evaluation of genome assemblies and assembly algorithms
- (2011) S. L. Salzberg et al. GENOME RESEARCH
- Paired de Bruijn Graphs: A Novel Approach for Incorporating Mate Pair Information into Genome Assemblers
- (2011) Paul Medvedev et al. JOURNAL OF COMPUTATIONAL BIOLOGY
- Opera: Reconstructing Optimal Genomic Scaffolds with High-Throughput Paired-End Sequences
- (2011) Song Gao et al. JOURNAL OF COMPUTATIONAL BIOLOGY
- Short Reads, Circular Genome: Skimming SOLiD Sequence to Construct the Bighorn Sheep Mitochondrial Genome
- (2011) Joshua M. Miller et al. JOURNAL OF HEREDITY
- Rapid hybrid de novo assembly of a microbial genome using only short reads: Corynebacterium pseudotuberculosis I19 as a case study
- (2011) Louise Teixeira Cerdeira et al. JOURNAL OF MICROBIOLOGICAL METHODS
- Comparative and demographic analysis of orang-utan genomes
- (2011) Devin P. Locke et al. NATURE
- Next-generation transcriptome assembly
- (2011) Jeffrey A. Martin et al. NATURE REVIEWS GENETICS
- Error and Error Mitigation in Low-Coverage Genome Assemblies
- (2011) Melissa J. Hubisz et al. PLoS One
- A Practical Comparison of De Novo Genome Assembly Software Tools for Next-Generation Sequencing Technologies
- (2011) Wenyu Zhang et al. PLoS One
- Comparing De Novo Genome Assembly: The Long and Short of It
- (2011) Giuseppe Narzisi et al. PLoS One
- Evaluation of Methods for De Novo Genome Assembly from High-Throughput Sequencing Reads Reveals Dependencies That Affect the Quality of the Results
- (2011) Niina Haiminen et al. PLoS One
- The Ecoresponsive Genome of Daphnia pulex
- (2011) J. K. Colbourne et al. SCIENCE
- HiTEC: accurate error correction in high-throughput sequencing data
- (2010) L. Ilie et al. BIOINFORMATICS
- Correction of sequencing errors in a mixed set of reads
- (2010) L. Salmela BIOINFORMATICS
- Efficient construction of an assembly string graph using the FM-index
- (2010) J. T. Simpson et al. BIOINFORMATICS
- Integrating genome assemblies with MAIA
- (2010) J. Nijkamp et al. BIOINFORMATICS
- Reptile: representative tiling for short read error correction
- (2010) X. Yang et al. BIOINFORMATICS
- Scaffolding pre-assembled contigs using SSPACE
- (2010) Marten Boetzer et al. BIOINFORMATICS
- SOPRA: Scaffolding algorithm for paired reads via statistical optimization
- (2010) Adel Dayarian et al. BMC BIOINFORMATICS
- De novo assembly of short sequence reads
- (2010) K. Paszkiewicz et al. BRIEFINGS IN BIOINFORMATICS
- Genome assembly quality: Assessment and improvement using the neutral indel model
- (2010) S. Meader et al. GENOME RESEARCH
- Assembly algorithms for next-generation sequencing data
- (2010) Jason R. Miller et al. GENOMICS
- Limitations of next-generation genome sequence assembly
- (2010) Can Alkan et al. NATURE METHODS
- High-quality draft assemblies of mammalian genomes from massively parallel sequence data
- (2010) S. Gnerre et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- The next-generation sequencing technology and application
- (2010) Xiaoguang Zhou et al. Protein & Cell
- SHREC: a short-read error correction method
- (2009) J. Schroder et al. BIOINFORMATICS
- A fast hybrid short read fragment assembly algorithm
- (2009) B. Schmidt et al. BIOINFORMATICS
- The Sequence Alignment/Map format and SAMtools
- (2009) H. Li et al. BIOINFORMATICS
- QSRA – a quality-value guided de novo short read assembler
- (2009) Douglas W Bryant et al. BMC BIOINFORMATICS
- Crystallizing short-read assemblies around seeds
- (2009) Mohammad Hossain et al. BMC BIOINFORMATICS
- Bos taurus genome assembly
- (2009) Yue Liu et al. BMC GENOMICS
- Genome assembly reborn: recent computational challenges
- (2009) M. Pop BRIEFINGS IN BIOINFORMATICS
- Next-Generation Sequencing: From Basic Research to Diagnostics
- (2009) K. V. Voelkerding et al. CLINICAL CHEMISTRY
- ABySS: A parallel assembler for short read sequence data
- (2009) J. T. Simpson et al. GENOME RESEARCH
- De novo assembly of human genomes with massively parallel short read sequencing
- (2009) R. Li et al. GENOME RESEARCH
- Maximum Likelihood Genome Assembly
- (2009) Paul Medvedev et al. JOURNAL OF COMPUTATIONAL BIOLOGY
- The sequence and de novo assembly of the giant panda genome
- (2009) Ruiqiang Li et al. NATURE
- Pebble and Rock Band: Heuristic Resolution of Repeats and Scaffolding in the Velvet Short-Read de Novo Assembler
- (2009) Daniel R. Zerbino et al. PLoS One
- Lineage-Specific Biology Revealed by a Finished Genome Assembly of the Mouse
- (2009) Deanna M. Church et al. PLOS BIOLOGY
- De novo genome sequence assembly of a filamentous fungus using Sanger, 454 and Illumina sequence data
- (2009) Scott DiGuistini et al. GENOME BIOLOGY
- ALLPATHS 2: small genomes assembled accurately and with high continuity from short paired reads
- (2009) Iain MacCallum et al. GENOME BIOLOGY
- Aggressive assembly of pyrosequencing reads with mates
- (2008) Jason R. Miller et al. BIOINFORMATICS
- De novo assembly using low-coverage short read sequence data from the rice pathogen Pseudomonas syringae pv. oryzae
- (2008) J. A. Reinhardt et al. GENOME RESEARCH
- De novo fragment assembly with short mate-paired reads: Does the read length matter?
- (2008) M. J. Chaisson et al. GENOME RESEARCH
- ALLPATHS: De novo assembly of whole-genome shotgun microreads
- (2008) J. Butler et al. GENOME RESEARCH
- De novo bacterial genome sequencing: Millions of very short reads assembled on a desktop computer
- (2008) D. Hernandez et al. GENOME RESEARCH
- Velvet: Algorithms for de novo short read assembly using de Bruijn graphs
- (2008) D. R. Zerbino et al. GENOME RESEARCH
- The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus)
- (2008) Ray Ming et al. NATURE
- Assessing the gene space in draft genomes
- (2008) Genis Parra et al. NUCLEIC ACIDS RESEARCH
- Genome assembly forensics: finding the elusive mis-assembly
- (2008) Adam M Phillippy et al. GENOME BIOLOGY
- Short read fragment assembly of bacterial genomes
- (2007) M. J. Chaisson et al. GENOME RESEARCH
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