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Items: 1 to 20 of 107

1.

BEDOPS: high-performance genomic feature operations.

Neph S, Kuehn MS, Reynolds AP, Haugen E, Thurman RE, Johnson AK, Rynes E, Maurano MT, Vierstra J, Thomas S, Sandstrom R, Humbert R, Stamatoyannopoulos JA.

Bioinformatics. 2012 Jul 15;28(14):1919-20. doi: 10.1093/bioinformatics/bts277. Epub 2012 May 9.

2.

Operating on Genomic Ranges Using BEDOPS.

Neph S, Reynolds AP, Kuehn MS, Stamatoyannopoulos JA.

Methods Mol Biol. 2016;1418:267-81. doi: 10.1007/978-1-4939-3578-9_14.

PMID:
27008020
3.

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.

4.

BEDTools: a flexible suite of utilities for comparing genomic features.

Quinlan AR, Hall IM.

Bioinformatics. 2010 Mar 15;26(6):841-2. doi: 10.1093/bioinformatics/btq033. Epub 2010 Jan 28.

5.

MetaCRAM: an integrated pipeline for metagenomic taxonomy identification and compression.

Kim M, Zhang X, Ligo JG, Farnoud F, Veeravalli VV, Milenkovic O.

BMC Bioinformatics. 2016 Feb 19;17:94. doi: 10.1186/s12859-016-0932-x.

6.

MFCompress: a compression tool for FASTA and multi-FASTA data.

Pinho AJ, Pratas D.

Bioinformatics. 2014 Jan 1;30(1):117-8. doi: 10.1093/bioinformatics/btt594. Epub 2013 Oct 16.

7.

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.

PMID:
22833526
8.

The human genome contracts again.

Pavlichin DS, Weissman T, Yona G.

Bioinformatics. 2013 Sep 1;29(17):2199-202. doi: 10.1093/bioinformatics/btt362. Epub 2013 Jun 22.

PMID:
23793748
9.

GenomicTools: a computational platform for developing high-throughput analytics in genomics.

Tsirigos A, Haiminen N, Bilal E, Utro F.

Bioinformatics. 2012 Jan 15;28(2):282-3. doi: 10.1093/bioinformatics/btr646. Epub 2011 Nov 22.

PMID:
22113082
10.

smallWig: parallel compression of RNA-seq WIG files.

Wang Z, Weissman T, Milenkovic O.

Bioinformatics. 2016 Jan 15;32(2):173-80. doi: 10.1093/bioinformatics/btv561. Epub 2015 Sep 30.

PMID:
26424856
11.

DNA-COMPACT: DNA COMpression based on a pattern-aware contextual modeling technique.

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

PLoS One. 2013 Nov 25;8(11):e80377. doi: 10.1371/journal.pone.0080377. eCollection 2013.

12.

BigWig and BigBed: enabling browsing of large distributed datasets.

Kent WJ, Zweig AS, Barber G, Hinrichs AS, Karolchik D.

Bioinformatics. 2010 Sep 1;26(17):2204-7. doi: 10.1093/bioinformatics/btq351. Epub 2010 Jul 17.

13.

Compression and fast retrieval of SNP data.

Sambo F, Di Camillo B, Toffolo G, Cobelli C.

Bioinformatics. 2014 Nov 1;30(21):3078-85. doi: 10.1093/bioinformatics/btu495. Epub 2014 Jul 26.

14.

iDoComp: a compression scheme for assembled genomes.

Ochoa I, Hernaez M, Weissman T.

Bioinformatics. 2015 Mar 1;31(5):626-33. doi: 10.1093/bioinformatics/btu698. Epub 2014 Oct 24.

PMID:
25344501
15.

NGC: lossless and lossy compression of aligned high-throughput sequencing data.

Popitsch N, von Haeseler A.

Nucleic Acids Res. 2013 Jan 7;41(1):e27. doi: 10.1093/nar/gks939. Epub 2012 Oct 12.

16.

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
17.

Lossy compression of quality scores in genomic data.

Cánovas R, Moffat A, Turpin A.

Bioinformatics. 2014 Aug 1;30(15):2130-6. doi: 10.1093/bioinformatics/btu183. Epub 2014 Apr 10.

PMID:
24728856
18.

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.

PMID:
22556365
19.

Track data hubs enable visualization of user-defined genome-wide annotations on the UCSC Genome Browser.

Raney BJ, Dreszer TR, Barber GP, Clawson H, Fujita PA, Wang T, Nguyen N, Paten B, Zweig AS, Karolchik D, Kent WJ.

Bioinformatics. 2014 Apr 1;30(7):1003-5. doi: 10.1093/bioinformatics/btt637. Epub 2013 Nov 13.

20.

On-Demand Indexing for Referential Compression of DNA Sequences.

Alves F, Cogo V, Wandelt S, Leser U, Bessani A.

PLoS One. 2015 Jul 6;10(7):e0132460. doi: 10.1371/journal.pone.0132460. eCollection 2015.

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