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Results: 1 to 20 of 105

1.

A novel and well-defined benchmarking method for second generation read mapping.

Holtgrewe M, Emde AK, Weese D, Reinert K.

BMC Bioinformatics. 2011 May 26;12:210. doi: 10.1186/1471-2105-12-210.

PMID:
21615913
[PubMed - indexed for MEDLINE]
Free PMC Article
2.

RazerS 3: faster, fully sensitive read mapping.

Weese D, Holtgrewe M, Reinert K.

Bioinformatics. 2012 Oct 15;28(20):2592-9. doi: 10.1093/bioinformatics/bts505. Epub 2012 Aug 24.

PMID:
22923295
[PubMed - indexed for MEDLINE]
Free Article
3.

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.

PMID:
24708189
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

RazerS--fast read mapping with sensitivity control.

Weese D, Emde AK, Rausch T, Döring A, Reinert K.

Genome Res. 2009 Sep;19(9):1646-54. doi: 10.1101/gr.088823.108. Epub 2009 Jul 10.

PMID:
19592482
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

A consistency-based consensus algorithm for de novo and reference-guided sequence assembly of short reads.

Rausch T, Koren S, Denisov G, Weese D, Emde AK, Döring A, Reinert K.

Bioinformatics. 2009 May 1;25(9):1118-24. doi: 10.1093/bioinformatics/btp131. Epub 2009 Mar 5.

PMID:
19269990
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

Efficient alignment of pyrosequencing reads for re-sequencing applications.

Fernandes F, da Fonseca PG, Russo LM, Oliveira AL, Freitas AT.

BMC Bioinformatics. 2011 May 16;12:163. doi: 10.1186/1471-2105-12-163.

PMID:
21672185
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

Specificity control for read alignments using an artificial reference genome-guided false discovery rate.

Giese SH, Zickmann F, Renard BY.

Bioinformatics. 2014 Jan 1;30(1):9-16. doi: 10.1093/bioinformatics/btt255. Epub 2013 May 17.

PMID:
23685787
[PubMed - indexed for MEDLINE]
8.

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.

PMID:
24499321
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

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.

PMID:
21989248
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

QC-Chain: fast and holistic quality control method for next-generation sequencing data.

Zhou Q, Su X, Wang A, Xu J, Ning K.

PLoS One. 2013;8(4):e60234. doi: 10.1371/journal.pone.0060234. Epub 2013 Apr 2.

PMID:
23565205
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

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.

PMID:
23758764
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

Anatomy of a hash-based long read sequence mapping algorithm for next generation DNA sequencing.

Misra S, Agrawal A, Liao WK, Choudhary A.

Bioinformatics. 2011 Jan 15;27(2):189-95. doi: 10.1093/bioinformatics/btq648. Epub 2010 Nov 18.

PMID:
21088030
[PubMed - indexed for MEDLINE]
Free Article
13.

Incorporating sequence quality data into alignment improves DNA read mapping.

Frith MC, Wan R, Horton P.

Nucleic Acids Res. 2010 Apr;38(7):e100. doi: 10.1093/nar/gkq010. Epub 2010 Jan 27.

PMID:
20110255
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

Tools for mapping high-throughput sequencing data.

Fonseca NA, Rung J, Brazma A, Marioni JC.

Bioinformatics. 2012 Dec 15;28(24):3169-77. doi: 10.1093/bioinformatics/bts605. Epub 2012 Oct 11.

PMID:
23060614
[PubMed - indexed for MEDLINE]
Free Article
15.

Indel-tolerant read mapping with trinucleotide frequencies using cache-oblivious kd-trees.

Mahmud MP, Wiedenhoeft J, Schliep A.

Bioinformatics. 2012 Sep 15;28(18):i325-i332. doi: 10.1093/bioinformatics/bts380.

PMID:
22962448
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

MicroRazerS: rapid alignment of small RNA reads.

Emde AK, Grunert M, Weese D, Reinert K, Sperling SR.

Bioinformatics. 2010 Jan 1;26(1):123-4. doi: 10.1093/bioinformatics/btp601. Epub 2009 Oct 29.

PMID:
19880369
[PubMed - indexed for MEDLINE]
Free Article
17.

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.

PMID:
21682852
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

De novo sequencing of plant genomes using second-generation technologies.

Imelfort M, Edwards D.

Brief Bioinform. 2009 Nov;10(6):609-18. doi: 10.1093/bib/bbp039. Review.

PMID:
19933209
[PubMed - indexed for MEDLINE]
Free Article
19.

An improved approach for accurate and efficient calling of structural variations with low-coverage sequence data.

Zhang J, Wang J, Wu Y.

BMC Bioinformatics. 2012 Apr 19;13 Suppl 6:S6. doi: 10.1186/1471-2105-13-S6-S6.

PMID:
22537045
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

CloudBurst: highly sensitive read mapping with MapReduce.

Schatz MC.

Bioinformatics. 2009 Jun 1;25(11):1363-9. doi: 10.1093/bioinformatics/btp236. Epub 2009 Apr 8.

PMID:
19357099
[PubMed - indexed for MEDLINE]
Free PMC Article

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