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Items: 1 to 20 of 566

1.

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.

2.

DELIMINATE--a fast and efficient method for loss-less compression of genomic sequences: sequence analysis.

Mohammed MH, Dutta A, Bose T, Chadaram S, Mande SS.

Bioinformatics. 2012 Oct 1;28(19):2527-9. Epub 2012 Jul 25.

3.

BEETL-fastq: a searchable compressed archive for DNA reads.

Janin L, Schulz-Trieglaff O, Cox AJ.

Bioinformatics. 2014 Oct;30(19):2796-801. doi: 10.1093/bioinformatics/btu387. Epub 2014 Jun 20.

4.

Reference-based compression of short-read sequences using path encoding.

Kingsford C, Patro R.

Bioinformatics. 2015 Jun 15;31(12):1920-8. doi: 10.1093/bioinformatics/btv071. Epub 2015 Feb 2.

5.

Data-dependent bucketing improves reference-free compression of sequencing reads.

Patro R, Kingsford C.

Bioinformatics. 2015 Sep 1;31(17):2770-7. doi: 10.1093/bioinformatics/btv248. Epub 2015 Apr 24.

6.

Data structures and compression algorithms for high-throughput sequencing technologies.

Daily K, Rigor P, Christley S, Xie X, Baldi P.

BMC Bioinformatics. 2010 Oct 14;11:514. doi: 10.1186/1471-2105-11-514.

7.

Fast lossless compression via cascading Bloom filters.

Rozov R, Shamir R, Halperin E.

BMC Bioinformatics. 2014;15 Suppl 9:S7. doi: 10.1186/1471-2105-15-S9-S7. Epub 2014 Sep 10.

8.

Large-scale compression of genomic sequence databases with the Burrows-Wheeler transform.

Cox AJ, Bauer MJ, Jakobi T, Rosone G.

Bioinformatics. 2012 Jun 1;28(11):1415-9. doi: 10.1093/bioinformatics/bts173. Epub 2012 May 3.

9.

LFQC: a lossless compression algorithm for FASTQ files.

Pathak S, Rajasekaran S.

Bioinformatics. 2014 Oct 24. pii: btu701. [Epub ahead of print]

10.

LFQC: a lossless compression algorithm for FASTQ files.

Nicolae M, Pathak S, Rajasekaran S.

Bioinformatics. 2015 Oct 15;31(20):3276-81. doi: 10.1093/bioinformatics/btv384. Epub 2015 Jun 20.

11.

QualComp: a new lossy compressor for quality scores based on rate distortion theory.

Ochoa I, Asnani H, Bharadia D, Chowdhury M, Weissman T, Yona G.

BMC Bioinformatics. 2013 Jun 8;14:187. doi: 10.1186/1471-2105-14-187.

12.

Compression of FASTQ and SAM format sequencing data.

Bonfield JK, Mahoney MV.

PLoS One. 2013;8(3):e59190. doi: 10.1371/journal.pone.0059190. Epub 2013 Mar 22.

13.

BIND - an algorithm for loss-less compression of nucleotide sequence data.

Bose T, Mohammed MH, Dutta A, Mande SS.

J Biosci. 2012 Sep;37(4):785-9.

14.

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.

15.

KungFQ: a simple and powerful approach to compress fastq files.

Grassi E, Di Gregorio F, Molineris I.

IEEE/ACM Trans Comput Biol Bioinform. 2012 Nov-Dec;9(6):1837-42. doi: 10.1109/TCBB.2012.123.

PMID:
23221092
16.

HUGO: Hierarchical mUlti-reference Genome cOmpression for aligned reads.

Li P, Jiang X, Wang S, Kim J, Xiong H, Ohno-Machado L.

J Am Med Inform Assoc. 2014 Mar-Apr;21(2):363-73. doi: 10.1136/amiajnl-2013-002147. Epub 2013 Dec 24.

17.

SRComp: short read sequence compression using burstsort and Elias omega coding.

Selva JJ, Chen X.

PLoS One. 2013 Dec 13;8(12):e81414. doi: 10.1371/journal.pone.0081414. eCollection 2013.

18.

Light-weight reference-based compression of FASTQ data.

Zhang Y, Li L, Yang Y, Yang X, He S, Zhu Z.

BMC Bioinformatics. 2015 Jun 9;16:188. doi: 10.1186/s12859-015-0628-7.

19.

MAFCO: a compression tool for MAF files.

Matos LM, Neves AJ, Pratas D, Pinho AJ.

PLoS One. 2015 Mar 27;10(3):e0116082. doi: 10.1371/journal.pone.0116082. eCollection 2015.

20.

Reference-free compression of high throughput sequencing data with a probabilistic de Bruijn graph.

Benoit G, Lemaitre C, Lavenier D, Drezen E, Dayris T, Uricaru R, Rizk G.

BMC Bioinformatics. 2015 Sep 14;16:288. doi: 10.1186/s12859-015-0709-7.

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