SHRiMP2: Sensitive yet Practical Short Read Mapping
作者： Matei David , Misko Dzamba , Dan Lister , Lucian Ilie , Michael Brudno
DOI: 10.1093/BIOINFORMATICS/BTR046
关键词: Computer engineering 、 Source code 、 Sensitivity (control systems) 、 Sequence alignment 、 Database 、 Computer science 、 DNA 、 Short read 、 Sequence analysis
摘要: We report on a major update (version 2) of the original SHort Read Mapping Program (SHRiMP). SHRiMP2 primarily targets mapping sensitivity, and is able to achieve high accuracy at …
oup.com
oxfordjournals.org
paperity.org参考文章(10)
Kim R. Rasmussen, Jens Stoye, Eugene W. Myers, Efficient Q-Gram Filters for Finding All Epsilon-Matches Over a Given Length Journal of Computational Biology. ,vol. 13, pp. 296- 308 ,(2006) , 10.1089/CMB.2006.13.296
Nils Homer, Barry Merriman, Stanley F. Nelson, BFAST: An Alignment Tool for Large Scale Genome Resequencing PLoS ONE. ,vol. 4, pp. e7767- 12 ,(2009) , 10.1371/JOURNAL.PONE.0007767
Kim R Rasmussen, Jens Stoye, Eugene W Myers, None, Efficient q -gram filters for finding all ε-matches over a given length research in computational molecular biology. ,vol. 3500, pp. 189- 203 ,(2005) , 10.1007/11415770_15
T.F. Smith, M.S. Waterman, Identification of common molecular subsequences. Journal of Molecular Biology. ,vol. 147, pp. 195- 197 ,(1981) , 10.1016/0022-2836(81)90087-5
H. Li, N. Homer, A survey of sequence alignment algorithms for next-generation sequencing. Briefings in Bioinformatics. ,vol. 11, pp. 473- 483 ,(2010) , 10.1093/BIB/BBQ015
T. D. Wu, S. Nacu, Fast and SNP-tolerant detection of complex variants and splicing in short reads Bioinformatics. ,vol. 26, pp. 873- 881 ,(2010) , 10.1093/BIOINFORMATICS/BTQ057
H. Li, R. Durbin, Fast and accurate short read alignment with Burrows–Wheeler transform Bioinformatics. ,vol. 25, pp. 1754- 1760 ,(2009) , 10.1093/BIOINFORMATICS/BTP324
L. Ilie, S. Ilie, Multiple spaced seeds for homology search Bioinformatics. ,vol. 23, pp. 2969- 2977 ,(2007) , 10.1093/BIOINFORMATICS/BTM422
Ben Langmead, Cole Trapnell, Mihai Pop, Steven L Salzberg, Ultrafast and memory-efficient alignment of short DNA sequences to the human genome Genome Biology. ,vol. 10, pp. 1- 10 ,(2009) , 10.1186/GB-2009-10-3-R25
Stephen M. Rumble, Phil Lacroute, Adrian V. Dalca, Marc Fiume, Arend Sidow, Michael Brudno, SHRiMP: Accurate Mapping of Short Color-space Reads PLoS Computational Biology. ,vol. 5, pp. e1000386- ,(2009) , 10.1371/JOURNAL.PCBI.1000386