Approaches and Challenges of Next-Generation Sequence Assembly Stages
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[1] Paul Medvedev,et al. Ab Initio Whole Genome Shotgun Assembly with Mated Short Reads , 2008, RECOMB.
[2] René L. Warren,et al. Assembling millions of short DNA sequences using SSAKE , 2006, Bioinform..
[3] Paul Medvedev,et al. Maximum Likelihood Genome Assembly , 2009, J. Comput. Biol..
[4] Lucian Ilie,et al. HiTEC: accurate error correction in high-throughput sequencing data , 2011, Bioinform..
[5] E. Birney,et al. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. , 2008, Genome research.
[6] James R. Knight,et al. Genome sequencing in microfabricated high-density picolitre reactors , 2005, Nature.
[7] Adam M. Phillippy,et al. Comparative genome assembly , 2004, Briefings Bioinform..
[8] Esko Ukkonen,et al. Fast scaffolding with small independent mixed integer programs , 2011, Bioinform..
[9] C. Nusbaum,et al. ALLPATHS: de novo assembly of whole-genome shotgun microreads. , 2008, Genome research.
[10] Weng-Keen Wong,et al. QSRA – a quality-value guided de novo short read assembler , 2009, BMC Bioinformatics.
[11] Kunihiko Sadakane,et al. Succinct de Bruijn Graphs , 2012, WABI.
[12] Thomas C. Conway,et al. Succinct data structures for assembling large genomes , 2010, Bioinform..
[13] 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.
[14] Eugene W. Myers,et al. Computability of Models for Sequence Assembly , 2007, WABI.
[15] S. Salzberg,et al. Hierarchical scaffolding with Bambus. , 2003, Genome research.
[16] Srinivas Aluru,et al. A survey of error-correction methods for next-generation sequencing , 2013, Briefings Bioinform..
[17] 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.
[18] Wing-Kin Sung,et al. Opera: Reconstructing Optimal Genomic Scaffolds with High-Throughput Paired-End Sequences , 2011, J. Comput. Biol..
[19] David Hernández,et al. De novo bacterial genome sequencing: millions of very short reads assembled on a desktop computer. , 2008, Genome research.
[20] Mihai Pop,et al. Exploiting sparseness in de novo genome assembly , 2012, BMC Bioinformatics.
[21] Adel Dayarian,et al. SOPRA: Scaffolding algorithm for paired reads via statistical optimization , 2010, BMC Bioinformatics.
[22] Sara El-Metwally,et al. Next-Generation Sequence Assembly: Four Stages of Data Processing and Computational Challenges , 2013, PLoS Comput. Biol..
[23] Rayan Chikhi,et al. Space-efficient and exact de Bruijn graph representation based on a Bloom filter , 2012, Algorithms for Molecular Biology.
[24] Sergey Koren,et al. Aggressive assembly of pyrosequencing reads with mates , 2008, Bioinform..
[25] Yongchao Liu,et al. Musket: a multistage k-mer spectrum-based error corrector for Illumina sequence data , 2013, Bioinform..
[26] Haixu Tang,et al. Fragment assembly with short reads , 2004, Bioinform..
[27] Jan Schröder,et al. Genome analysis SHREC : a short-read error correction method , 2009 .
[28] David R. Kelley,et al. Quake: quality-aware detection and correction of sequencing errors , 2010, Genome Biology.
[29] M. Schatz,et al. Hybrid error correction and de novo assembly of single-molecule sequencing reads , 2012, Nature Biotechnology.
[30] Andrew H. Chan,et al. ECHO: a reference-free short-read error correction algorithm. , 2011, Genome research.
[31] Zhong Wang,et al. Next-generation transcriptome assembly , 2011, Nature Reviews Genetics.
[32] 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.
[33] Mark J. P. Chaisson,et al. Short read fragment assembly of bacterial genomes. , 2008, Genome research.
[34] Steven Skiena,et al. Crystallizing short-read assemblies around seeds , 2009, BMC Bioinformatics.
[35] Jared T. Simpson,et al. Efficient construction of an assembly string graph using the FM-index , 2010, Bioinform..
[36] S. Koren,et al. Assembly algorithms for next-generation sequencing data. , 2010, Genomics.
[37] Paul Medvedev,et al. Error correction of high-throughput sequencing datasets with non-uniform coverage , 2011, Bioinform..
[38] Steven J. M. Jones,et al. Abyss: a Parallel Assembler for Short Read Sequence Data Material Supplemental Open Access , 2022 .
[39] Huanming Yang,et al. De novo assembly of human genomes with massively parallel short read sequencing. , 2010, Genome research.
[40] Nilgun Donmez,et al. SCARPA: scaffolding reads with practical algorithms , 2013, Bioinform..
[41] Eugene W. Myers,et al. The fragment assembly string graph , 2005, ECCB/JBI.
[42] Stefan Kurtz,et al. Readjoiner: a fast and memory efficient string graph-based sequence assembler , 2012, BMC Bioinformatics.
[43] Jan Schröder,et al. BIOINFORMATICS ORIGINAL PAPER , 2022 .
[44] Leena Salmela,et al. Correction of sequencing errors in a mixed set of reads , 2010, Bioinform..
[45] A. Gnirke,et al. High-quality draft assemblies of mammalian genomes from massively parallel sequence data , 2010, Proceedings of the National Academy of Sciences.
[46] Paul Medvedev,et al. Paired de Bruijn Graphs: A Novel Approach for Incorporating Mate Pair Information into Genome Assemblers , 2011, J. Comput. Biol..
[47] Marcel J. T. Reinders,et al. GRASS: a generic algorithm for scaffolding next-generation sequencing assemblies , 2012, Bioinform..
[48] Pavel A. Pevzner,et al. From de Bruijn Graphs to Rectangle Graphs for Genome Assembly , 2012, WABI.
[49] Eugene W. Myers,et al. A whole-genome assembly of Drosophila. , 2000, Science.
[50] R. Durbin,et al. Efficient de novo assembly of large genomes using compressed data structures. , 2012, Genome research.
[51] Walter Pirovano,et al. BIOINFORMATICS APPLICATIONS , 2022 .
[52] Bertil Schmidt,et al. A fast hybrid short read fragment assembly algorithm , 2009, Bioinform..
[53] Eugene W. Myers,et al. The greedy path-merging algorithm for contig scaffolding , 2002, JACM.
[54] Gregory Kucherov,et al. Using cascading Bloom filters to improve the memory usage for de Brujin graphs , 2013, Algorithms for Molecular Biology.
[55] Juliane C. Dohm,et al. SHARCGS, a fast and highly accurate short-read assembly algorithm for de novo genomic sequencing. , 2007, Genome research.
[56] Vincent J. Magrini,et al. Extending assembly of short DNA sequences to handle error , 2007, Bioinform..
[57] 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.
[58] Sergey Koren,et al. Bambus 2: scaffolding metagenomes , 2011, Bioinform..
[59] Srinivas Aluru,et al. Reptile: representative tiling for short read error correction , 2010, Bioinform..
[60] Mark J. P. Chaisson,et al. De novo fragment assembly with short mate-paired reads: Does the read length matter? , 2009, Genome research.
[61] Qingpeng Zhang,et al. These Are Not the K-mers You Are Looking For: Efficient Online K-mer Counting Using a Probabilistic Data Structure , 2013, PloS one.
[62] A. Gnirke,et al. ALLPATHS 2: small genomes assembled accurately and with high continuity from short paired reads , 2009, Genome Biology.