No-reference compression of genomic data stored in FASTQ format

Proceedings - 2011 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2011

Volumn , Issue , 2011, Pages 147-150

  Bhola, Vishal ^a   Bopardikar, Ajit S ^a   Narayanan, Rangavittal ^a   Lee, Kyusang ^b   Ahn, Taejin ^b  

^a Samsung Electronics India Software Operations Ltd   (India)

^b SAMSUNG Electronics   (South Korea)

Author keywords

FASTQ; Genomic Data Compression; Next generation sequencing

Indexed keywords

COMPRESSION SYSTEM; ENTROPY CODING; FASTQ; GENOMIC DATA; NEXT GENERATION SEQUENCING; NO REFERENCES; QUALITY DATA; QUALITY INFORMATION; QUALITY VALUE; RUN LENGTH; TEXT COMPRESSIONS; TEXT DATA;

BENCHMARKING; BIOINFORMATICS; ENCODING (SYMBOLS); GENES;

DATA COMPRESSION;

EID: 84862938045     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/BIBM.2011.110     Document Type: Conference Paper

References (8)

1. W. J. Ansorge, "Next-generation DNA sequencing techniques," New Biotechnology, vol. 25, no. 4, pp. 195-203, 2009.
2. R. Giancarlo, D. Scaturro, and F. Utro, "Textual data compression in computational biology: a synopsis," Bioinformatics, vol. 25, no. 13, pp. 1575-1586, 2009.
3. P. J. A. Cock, C. J. Fields, N. Goto, M. L. Heuer, and P. M. Rice, "The sanger fastq file format for sequences with quality scores, and the solexa/illumina fastq variants," Nucleic Acids Research, vol. 38, no. 6, pp. 1767-1771, 2010.
4. M. H.-Y. Fritz, R. Leinonen, G. Cochrane, and E. Birney, "Efficient storage of high throughput sequencing data using reference-based compression," Genome Research, 2011.
5. W. Tembe and J. L. E. Suh, "G-sqz: compact encoding of genomic sequence and quality data," Bioinformatics, vol. 26, no. 17, pp. 2192-2194, 2010.
6. S. Deorowicz and S. Grabowski, "Compression of genomic sequences in FASTQ format," Bioinformatics, 2011.
7. Http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html.
8. K. Kaipa, A. S. Bopardikar, S. Abhilash, P. Venkataraman, K. S. Lee, T. J. Ahn, and R. Narayanan, "Algorithm for dna sequence compression based on prediction of mismatch bases and repeat location," in Bioinformatics and Biomedicine (BIBM), 2010 IEEE International Conference on, December 2010, pp. 851 -852.