Next Generation Sequencing Technologies and Challenges in Sequence Assembly
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[1] David Hernández,et al. De novo bacterial genome sequencing: millions of very short reads assembled on a desktop computer. , 2008, Genome research.
[2] A. Gnirke,et al. ALLPATHS 2: small genomes assembled accurately and with high continuity from short paired reads , 2009, Genome Biology.
[3] Eugene W. Myers,et al. The fragment assembly string graph , 2005, ECCB/JBI.
[4] Mihai Pop,et al. Exploiting sparseness in de novo genome assembly , 2012, BMC Bioinformatics.
[5] Peter A. Meric,et al. Lineage-Specific Biology Revealed by a Finished Genome Assembly of the Mouse , 2009, PLoS biology.
[6] Todd H. Oakley,et al. The Ecoresponsive Genome of Daphnia pulex , 2011, Science.
[7] Kamil Khanipov,et al. Slim-Filter: an interactive windows-based application for illumina genome analyzer data assessment and manipulation , 2012, BMC Bioinformatics.
[8] J. Todd,et al. Rare Variants of IFIH1, a Gene Implicated in Antiviral Responses, Protect Against Type 1 Diabetes , 2009, Science.
[9] Albert J. Vilella,et al. Comparative and demographic analysis of orang-utan genomes , 2011, Nature.
[10] Zhong Wang,et al. Next-generation transcriptome assembly , 2011, Nature Reviews Genetics.
[11] Dawei Li,et al. The sequence and de novo assembly of the giant panda genome , 2010, Nature.
[12] Steven Skiena,et al. Crystallizing short-read assemblies around seeds , 2009, BMC Bioinformatics.
[13] P. Pevzner,et al. De Novo Repeat Classification and Fragment Assembly , 2004 .
[14] Sergey Koren,et al. Bambus 2: scaffolding metagenomes , 2011, Bioinform..
[15] Juliane C. Dohm,et al. SHARCGS, a fast and highly accurate short-read assembly algorithm for de novo genomic sequencing. , 2007, Genome research.
[16] Srinivas Aluru,et al. Reptile: representative tiling for short read error correction , 2010, Bioinform..
[17] Sergey I. Nikolenko,et al. SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing , 2012, J. Comput. Biol..
[18] Alison S. Waller,et al. Assessment of Metagenomic Assembly Using Simulated Next Generation Sequencing Data , 2012, PloS one.
[19] Christoph Dieterich,et al. De novo assembly and validation of planaria transcriptome by massive parallel sequencing and shotgun proteomics. , 2011, Genome research.
[20] Alexey A. Gurevich,et al. QUAST: quality assessment tool for genome assemblies , 2013, Bioinform..
[21] S. Salzberg,et al. Hierarchical scaffolding with Bambus. , 2003, Genome research.
[22] Andrew H. Chan,et al. ECHO: a reference-free short-read error correction algorithm. , 2011, Genome research.
[23] Lucian Ilie,et al. HiTEC: accurate error correction in high-throughput sequencing data , 2011, Bioinform..
[24] H. Zoghbi,et al. Neurogenetics: Advancing the “Next-Generation” of Brain Research , 2010, Neuron.
[25] Manolis Kellis,et al. Error and Error Mitigation in Low-Coverage Genome Assemblies , 2011, PloS one.
[26] I. Rigoutsos,et al. Evaluation of Methods for De Novo Genome Assembly from High-Throughput Sequencing Reads Reveals Dependencies That Affect the Quality of the Results , 2011, PloS one.
[27] René L. Warren,et al. Assembling millions of short DNA sequences using SSAKE , 2006, Bioinform..
[28] Thomas C. Conway,et al. Succinct data structures for assembling large genomes , 2010, Bioinform..
[29] Jan Schröder,et al. BIOINFORMATICS ORIGINAL PAPER , 2022 .
[30] Andreas Tauch,et al. Rapid hybrid de novo assembly of a microbial genome using only short reads: Corynebacterium pseudotuberculosis I19 as a case study. , 2011, Journal of microbiological methods.
[31] Inanç Birol,et al. Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species , 2013, GigaScience.
[32] Bertil Schmidt,et al. A fast hybrid short read fragment assembly algorithm , 2009, Bioinform..
[33] Srinivas Aluru,et al. A survey of error-correction methods for next-generation sequencing , 2013, Briefings Bioinform..
[34] Adam M. Phillippy,et al. Comparative genome assembly , 2004, Briefings Bioinform..
[35] Mihai Pop,et al. Genome assembly reborn: recent computational challenges , 2009, Briefings Bioinform..
[36] Nilgun Donmez,et al. SCARPA: scaffolding reads with practical algorithms , 2013, Bioinform..
[37] Huanming Yang,et al. De novo assembly of human genomes with massively parallel short read sequencing. , 2010, Genome research.
[38] Jian Wang,et al. SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler , 2012, GigaScience.
[39] M. Pop,et al. Sequence assembly demystified , 2013, Nature Reviews Genetics.
[40] Siu-Ming Yiu,et al. IDBA - A Practical Iterative de Bruijn Graph De Novo Assembler , 2010, RECOMB.
[41] Thomas Wetter,et al. Genome Sequence Assembly Using Trace Signals and Additional Sequence Information , 1999, German Conference on Bioinformatics.
[42] Steven J. M. Jones,et al. De novo genome sequence assembly of a filamentous fungus using Sanger, 454 and Illumina sequence data , 2009, Genome Biology.
[43] Torsten Seemann,et al. VAGUE: a graphical user interface for the Velvet assembler , 2013, Bioinform..
[44] Paul Medvedev,et al. Ab Initio Whole Genome Shotgun Assembly with Mated Short Reads , 2008, RECOMB.
[45] Huzefa Rangwala,et al. Evaluation of short read metagenomic assembly , 2010, 2010 IEEE International Conference on Bioinformatics and Biomedicine (BIBM).
[46] S. B. Needleman,et al. A general method applicable to the search for similarities in the amino acid sequence of two proteins. , 1970, Journal of molecular biology.
[47] Haixu Tang,et al. Fragment assembly with short reads , 2004, Bioinform..
[48] E. Eichler,et al. Limitations of next-generation genome sequence assembly , 2011, Nature Methods.
[49] M. Schatz,et al. Algorithms Gage: a Critical Evaluation of Genome Assemblies and Assembly Material Supplemental , 2008 .
[50] Haixu Tang,et al. Fragment assembly with double-barreled data , 2001, ISMB.
[51] Jan Schröder,et al. Genome analysis SHREC : a short-read error correction method , 2009 .
[52] Leena Salmela,et al. Correction of sequencing errors in a mixed set of reads , 2010, Bioinform..
[53] A. Gnirke,et al. High-quality draft assemblies of mammalian genomes from massively parallel sequence data , 2010, Proceedings of the National Academy of Sciences.
[54] Keith Bradnam,et al. Assessing the gene space in draft genomes , 2008, Nucleic acids research.
[55] Miron Livny,et al. Validation of rice genome sequence by optical mapping , 2007, BMC Genomics.
[56] Heng Li,et al. Exploring single-sample SNP and INDEL calling with whole-genome de novo assembly , 2012, Bioinform..
[57] Esko Ukkonen,et al. Fast scaffolding with small independent mixed integer programs , 2011, Bioinform..
[58] G. Sherlock,et al. Rnnotator: an automated de novo transcriptome assembly pipeline from stranded RNA-Seq reads , 2010, BMC Genomics.
[59] E. Myers,et al. Basic local alignment search tool. , 1990, Journal of molecular biology.
[60] Eugene W. Myers,et al. The greedy path-merging algorithm for contig scaffolding , 2002, JACM.
[61] Weng-Keen Wong,et al. QSRA – a quality-value guided de novo short read assembler , 2009, BMC Bioinformatics.
[62] Sara El-Metwally,et al. Next-Generation Sequence Assembly: Four Stages of Data Processing and Computational Challenges , 2013, PLoS Comput. Biol..
[63] Mihai Pop,et al. Minimus: a fast, lightweight genome assembler , 2007, BMC Bioinformatics.
[64] Ruiqiang Li,et al. SOAP: short oligonucleotide alignment program , 2008, Bioinform..
[65] M. Schatz,et al. Hybrid error correction and de novo assembly of single-molecule sequencing reads , 2012, Nature Biotechnology.
[66] Sergey Koren,et al. Aggressive assembly of pyrosequencing reads with mates , 2008, Bioinform..
[67] Siu-Ming Yiu,et al. IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth , 2012, Bioinform..
[68] M. Berriman,et al. REAPR: a universal tool for genome assembly evaluation , 2013, Genome Biology.
[69] N. Friedman,et al. Trinity: reconstructing a full-length transcriptome without a genome from RNA-Seq data , 2011, Nature Biotechnology.
[70] Steven J. M. Jones,et al. Abyss: a Parallel Assembler for Short Read Sequence Data Material Supplemental Open Access , 2022 .
[71] James A. Cuff,et al. Genome sequence, comparative analysis and haplotype structure of the domestic dog , 2005, Nature.
[72] Eugene W. Myers,et al. Computability of Models for Sequence Assembly , 2007, WABI.
[73] François Laviolette,et al. Ray: Simultaneous Assembly of Reads from a Mix of High-Throughput Sequencing Technologies , 2010, J. Comput. Biol..
[74] Xuan Li,et al. Optimizing hybrid assembly of next-generation sequence data from Enterococcus faecium: a microbe with highly divergent genome , 2012, BMC Systems Biology.
[75] David R. Kelley,et al. Quake: quality-aware detection and correction of sequencing errors , 2010, Genome Biology.
[76] Paul Medvedev,et al. Paired de Bruijn Graphs: A Novel Approach for Incorporating Mate Pair Information into Genome Assemblers , 2011, J. Comput. Biol..
[77] Siu-Ming Yiu,et al. Meta-IDBA: a de Novo assembler for metagenomic data , 2011, Bioinform..
[78] Steven Salzberg,et al. GAGE-B: an evaluation of genome assemblers for bacterial organisms , 2013, Bioinform..
[79] P. Pevzner,et al. An Eulerian path approach to DNA fragment assembly , 2001, Proceedings of the National Academy of Sciences of the United States of America.
[80] C. Ponting,et al. Genome assembly quality: assessment and improvement using the neutral indel model. , 2010, Genome research.
[81] Eugene W. Myers,et al. Comparing Assemblies Using Fragments and Mate-Pairs , 2001, WABI.
[82] Mark J. P. Chaisson,et al. Short read fragment assembly of bacterial genomes. , 2008, Genome research.
[83] S. Kurtz,et al. Readjoiner: a fast and memory efficient string graph-based sequence assembler , 2012, BMC Bioinformatics.
[84] Walter Pirovano,et al. BIOINFORMATICS APPLICATIONS , 2022 .
[85] Marcel J. T. Reinders,et al. GRASS: a generic algorithm for scaffolding next-generation sequencing assemblies , 2012, Bioinform..
[86] Stephen M. Mount,et al. The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus) , 2008, Nature.
[87] Hui Shen,et al. Comparative studies of de novo assembly tools for next-generation sequencing technologies , 2011, Bioinform..
[88] Zhong Wang,et al. ALE: a generic assembly likelihood evaluation framework for assessing the accuracy of genome and metagenome assemblies , 2013, Bioinform..
[89] Martin Vingron,et al. Oases: robust de novo RNA-seq assembly across the dynamic range of expression levels , 2012, Bioinform..
[90] B. Mishra,et al. Feature-by-Feature – Evaluating De Novo Sequence Assembly , 2012, PloS one.
[91] E. Birney,et al. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. , 2008, Genome research.
[92] Paul Medvedev,et al. Maximum Likelihood Genome Assembly , 2009, J. Comput. Biol..
[93] Pavel A. Pevzner,et al. From de Bruijn Graphs to Rectangle Graphs for Genome Assembly , 2012, WABI.
[94] Paul Medvedev,et al. Error correction of high-throughput sequencing datasets with non-uniform coverage , 2011, Bioinform..
[95] B. Mishra,et al. Comparing De Novo Genome Assembly: The Long and Short of It , 2011, PloS one.
[96] Wing-Kin Sung,et al. Opera: Reconstructing Optimal Genomic Scaffolds with High-Throughput Paired-End Sequences , 2011, RECOMB.
[97] Nuno A. Fonseca,et al. Assemblathon 1: a competitive assessment of de novo short read assembly methods. , 2011, Genome research.
[98] S. Koren,et al. Assembly algorithms for next-generation sequencing data. , 2010, Genomics.
[99] Bairong Shen,et al. A Practical Comparison of De Novo Genome Assembly Software Tools for Next-Generation Sequencing Technologies , 2011, PloS one.
[100] K. McElreavey,et al. New Technologies for the Identification of Novel Genetic Markers of Disorders of Sex Development (DSD) , 2010, Sexual Development.
[101] Eugene W. Myers,et al. A whole-genome assembly of Drosophila. , 2000, Science.
[102] C. Nusbaum,et al. ALLPATHS: de novo assembly of whole-genome shotgun microreads. , 2008, Genome research.
[103] L. Pachter,et al. CGAL: computing genome assembly likelihoods , 2013 .
[104] Yongchao Liu,et al. Musket: a multistage k-mer spectrum-based error corrector for Illumina sequence data , 2013, Bioinform..
[105] Daniel R. Zerbino,et al. Pebble and Rock Band: Heuristic Resolution of Repeats and Scaffolding in the Velvet Short-Read de Novo Assembler , 2009, PloS one.
[106] Vincent J. Magrini,et al. Extending assembly of short DNA sequences to handle error , 2007, Bioinform..
[107] Adel Dayarian,et al. SOPRA: Scaffolding algorithm for paired reads via statistical optimization , 2010, BMC Bioinformatics.
[108] James R. Knight,et al. Genome sequencing in microfabricated high-density picolitre reactors , 2005, Nature.