Opera: Reconstructing Optimal Genomic Scaffolds with High-Throughput Paired-End Sequences
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[1] Jens Stoye,et al. Phylogenetic comparative assembly , 2009, Algorithms for Molecular Biology.
[2] Mark J. P. Chaisson,et al. De novo fragment assembly with short mate-paired reads: Does the read length matter? , 2009, Genome research.
[3] Eugene W. Myers,et al. A whole-genome assembly of Drosophila. , 2000, Science.
[4] J. Mullikin,et al. The phusion assembler. , 2003, Genome research.
[5] Haixu Tang,et al. Fragment assembly with double-barreled data , 2001, ISMB.
[6] 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.
[7] A. Gnirke,et al. ALLPATHS 2: small genomes assembled accurately and with high continuity from short paired reads , 2009, Genome Biology.
[8] Paramvir S. Dehal,et al. Whole-Genome Shotgun Assembly and Analysis of the Genome of Fugu rubripes , 2002, Science.
[9] Mihai Pop,et al. Shotgun Sequence Assembly , 2004, Adv. Comput..
[10] Daniel H. Huson,et al. BIOINFORMATICS ORIGINAL PAPER doi:10.1093/bioinformatics/btm153 Genome analysis OSLay: optimal syntenic layout of unfinished assemblies , 2022 .
[11] Gregory A Petsko,et al. Too big to succeed? , 2009, Genome Biology.
[12] Daniel H. Huson,et al. MetaSim—A Sequencing Simulator for Genomics and Metagenomics , 2008, PloS one.
[13] S. Salzberg,et al. Hierarchical scaffolding with Bambus. , 2003, Genome research.
[14] Yi Xing,et al. Negative selection pressure against premature protein truncation is reduced by both alternative splicing and diploidy , 2004, Genome Biology.
[15] E. Mauceli,et al. Whole-genome sequence assembly for mammalian genomes: Arachne 2. , 2003, Genome research.
[16] Eugene W. Myers,et al. The greedy path-merging algorithm for contig scaffolding , 2002, JACM.
[17] Mihai Pop,et al. Scaffolding and validation of bacterial genome assemblies using optical restriction maps , 2008, Bioinform..
[18] S. Salzberg,et al. Versatile and open software for comparing large genomes , 2004, Genome Biology.
[19] Adel Dayarian,et al. SOPRA: Scaffolding algorithm for paired reads via statistical optimization , 2010, BMC Bioinformatics.
[20] L. Du,et al. Multiplex sequencing of paired-end ditags (MS-PET): a strategy for the ultra-high-throughput analysis of transcriptomes and genomes , 2006, Nucleic acids research.
[21] S. Turner,et al. Real-Time DNA Sequencing from Single Polymerase Molecules , 2009, Science.
[22] Adam M. Phillippy,et al. Comparative genome assembly , 2004, Briefings Bioinform..
[23] James B. Saxe,et al. Dynamic-Programming Algorithms for Recognizing Small-Bandwidth Graphs in Polynomial Time , 1980, SIAM J. Algebraic Discret. Methods.
[24] D. Haussler,et al. Assembly of the working draft of the human genome with GigAssembler. , 2001, Genome research.
[25] Rasmus Wernersson,et al. FeatureMap3D—a tool to map protein features and sequence conservation onto homologous structures in the PDB , 2006, Nucleic Acids Res..
[26] Huilin Yang,et al. Whole-Genome Shotgun Assembly and Analysis of the Genome of Streptomyces mobaraensis DSM 40847, a Strain for Industrial Production of Microbial Transglutaminase , 2013, Genome Announcements.
[27] S. Turner,et al. Real-time DNA sequencing from single polymerase molecules. , 2010, Methods in enzymology.
[28] Donald Goldfarb,et al. A numerically stable dual method for solving strictly convex quadratic programs , 1983, Math. Program..
[29] Wing-Kin Sung,et al. A Genomic Survey of Positive Selection in Burkholderia pseudomallei Provides Insights into the Evolution of Accidental Virulence , 2010, PLoS pathogens.