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Items: 1 to 20 of 190

1.

mrsFAST-Ultra: a compact, SNP-aware mapper for high performance sequencing applications.

Hach F, Sarrafi I, Hormozdiari F, Alkan C, Eichler EE, Sahinalp SC.

Nucleic Acids Res. 2014 Jul;42(Web Server issue):W494-500. doi: 10.1093/nar/gku370. Epub 2014 May 8.

2.

Ψ-RA: a parallel sparse index for genomic read alignment.

Oğuzhan Külekci M, Hon WK, Shah R, Scott Vitter J, Xu B.

BMC Genomics. 2011;12 Suppl 2:S7. doi: 10.1186/1471-2164-12-S2-S7. Epub 2011 Jul 27.

3.

Hobbes: optimized gram-based methods for efficient read alignment.

Ahmadi A, Behm A, Honnalli N, Li C, Weng L, Xie X.

Nucleic Acids Res. 2012 Mar;40(6):e41. doi: 10.1093/nar/gkr1246. Epub 2011 Dec 22.

4.

SCALCE: boosting sequence compression algorithms using locally consistent encoding.

Hach F, Numanagic I, Alkan C, Sahinalp SC.

Bioinformatics. 2012 Dec 1;28(23):3051-7. doi: 10.1093/bioinformatics/bts593. Epub 2012 Oct 9.

5.

Improving read mapping using additional prefix grams.

Kim J, Li C, Xie X.

BMC Bioinformatics. 2014 Feb 5;15:42. doi: 10.1186/1471-2105-15-42.

6.

Benchmarking short sequence mapping tools.

Hatem A, Bozdağ D, Toland AE, Çatalyürek ÜV.

BMC Bioinformatics. 2013 Jun 7;14:184. doi: 10.1186/1471-2105-14-184.

7.

Accurate estimation of short read mapping quality for next-generation genome sequencing.

Ruffalo M, Koyutürk M, Ray S, LaFramboise T.

Bioinformatics. 2012 Sep 15;28(18):i349-i355. doi: 10.1093/bioinformatics/bts408.

8.

Sensitive and fast mapping of di-base encoded reads.

Hormozdiari F, Hach F, Sahinalp SC, Eichler EE, Alkan C.

Bioinformatics. 2011 Jul 15;27(14):1915-21. doi: 10.1093/bioinformatics/btr303. Epub 2011 May 17. Erratum in: Bioinformatics. 2012 Jan 1;28(1):150.

9.

Querying large read collections in main memory: a versatile data structure.

Philippe N, Salson M, Lecroq T, Léonard M, Commes T, Rivals E.

BMC Bioinformatics. 2011 Jun 17;12:242. doi: 10.1186/1471-2105-12-242.

10.

An investigation of causes of false positive single nucleotide polymorphisms using simulated reads from a small eukaryote genome.

Ribeiro A, Golicz A, Hackett CA, Milne I, Stephen G, Marshall D, Flavell AJ, Bayer M.

BMC Bioinformatics. 2015 Nov 11;16:382. doi: 10.1186/s12859-015-0801-z.

11.

Evaluation and assessment of read-mapping by multiple next-generation sequencing aligners based on genome-wide characteristics.

Thankaswamy-Kosalai S, Sen P, Nookaew I.

Genomics. 2017 Jul;109(3-4):186-191. doi: 10.1016/j.ygeno.2017.03.001. Epub 2017 Mar 9.

PMID:
28286147
12.

Comparative analysis of algorithms for next-generation sequencing read alignment.

Ruffalo M, LaFramboise T, Koyutürk M.

Bioinformatics. 2011 Oct 15;27(20):2790-6. doi: 10.1093/bioinformatics/btr477. Epub 2011 Aug 19.

PMID:
21856737
13.

Re-alignment of the unmapped reads with base quality score.

Peng X, Wang J, Zhang Z, Xiao Q, Li M, Pan Y.

BMC Bioinformatics. 2015;16 Suppl 5:S8. doi: 10.1186/1471-2105-16-S5-S8. Epub 2015 Mar 18.

14.

NextGenMap: fast and accurate read mapping in highly polymorphic genomes.

Sedlazeck FJ, Rescheneder P, von Haeseler A.

Bioinformatics. 2013 Nov 1;29(21):2790-1. doi: 10.1093/bioinformatics/btt468. Epub 2013 Aug 23.

PMID:
23975764
15.

Fast and accurate mapping of Complete Genomics reads.

Lee D, Hormozdiari F, Xin H, Hach F, Mutlu O, Alkan C.

Methods. 2015 Jun;79-80:3-10. doi: 10.1016/j.ymeth.2014.10.012. Epub 2014 Oct 22.

16.

Comparison of mapping algorithms used in high-throughput sequencing: application to Ion Torrent data.

Caboche S, Audebert C, Lemoine Y, Hot D.

BMC Genomics. 2014 Apr 5;15:264. doi: 10.1186/1471-2164-15-264.

17.

SInC: an accurate and fast error-model based simulator for SNPs, Indels and CNVs coupled with a read generator for short-read sequence data.

Pattnaik S, Gupta S, Rao AA, Panda B.

BMC Bioinformatics. 2014 Feb 5;15:40. doi: 10.1186/1471-2105-15-40.

18.

BamView: visualizing and interpretation of next-generation sequencing read alignments.

Carver T, Harris SR, Otto TD, Berriman M, Parkhill J, McQuillan JA.

Brief Bioinform. 2013 Mar;14(2):203-12. doi: 10.1093/bib/bbr073. Epub 2012 Jan 16.

19.

Meta-aligner: long-read alignment based on genome statistics.

Nashta-Ali D, Aliyari A, Ahmadian Moghadam A, Edrisi MA, Motahari SA, Hossein Khalaj B.

BMC Bioinformatics. 2017 Feb 23;18(1):126. doi: 10.1186/s12859-017-1518-y.

20.

Concurrent and Accurate Short Read Mapping on Multicore Processors.

Martínez H, Tárraga J, Medina I, Barrachina S, Castillo M, Dopazo J, Quintana-Ortí ES.

IEEE/ACM Trans Comput Biol Bioinform. 2015 Sep-Oct;12(5):995-1007. doi: 10.1109/TCBB.2015.2392077.

PMID:
26451814

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