Compression of FASTQ and SAM Format Sequencing Data

PLoS ONE

Volumn 8, Issue 3, 2013, Pages

  Bonfield, James K ^a   Mahoney, Matthew V ^b  

^a WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

^b DELL INC   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; COMPUTER MEMORY; CONTROLLED STUDY; DATA ANALYSIS; DATA ANALYSIS SOFTWARE; FASTQ FILE FORMAT; GENETIC ALGORITHM; GENETIC DATABASE; REFERENCE DATABASE; SAM FILE FORMAT; SEQUENCE ANALYSIS; SEQUENCE DATABASE;

COMPUTATIONAL BIOLOGY; DATA COMPRESSION; SEQUENCE ANALYSIS, DNA; SOFTWARE;

EID: 84875363204     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0059190     Document Type: Article

References (33)

1. Cochrane G, Cook CE, Birney E, (2012) The future of dna sequence archiving. GigaScience 1: 2.
2. Cock PJA, Fields CJ, Goto N, Heuer ML, Rice PM, (2010) The sanger FASTQ format for sequences with quality scores, and the Solexa/fillumina FASTQ variants. Nucleic Acids Research 38: 1767-1771.
3. Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, et al. (2005) Genome sequencing in microfabricated high-density picolitre reactors. Nature 437: 376-380.
4. Pandey V, Nutter RC, Prediger E (2008) Next-Generation Genome Sequencing, Berlin, Germany: Wiley- VCH, chapter Applied Biosystems SOLiD System: Ligation-Based Sequencing. 29-41.
5. Bentley DR, Balasubramanian S, Swerdlow HP, Smith GP, Milton J, et al. (2008) Accurate whole human genome sequencing using reversible terminator chemistry. Nature 456: 53-59.
6. Cox AJ, Bauer MJ, Jakobi T, Rosone G, (2012) Large-scale compression of genomic sequence databases with the Burrows-Wheeler transform. Bioinformatics 28: 1415-1419.
7. Pinho AJ, Pratas D, Garcia SP, (2012) GReEn: a tool for efficient compression of genome resequencing data. Nucleic Acids Research 40: 27.
8. Asnani H, Bharadia D, Chowdhury M, Ochoa I, Sharon I, et al. (2012) Lossy compression of quality values via rate distortion theory. arXiv preprint arXiv:12075184.
9. Wan R, Anh VN, Asai K, (2012) Transformations for the compression of FASTQ quality scores of next-generation sequencing data. Bioinformatics 28: 628-635.
10. Tembe W, Lowey J, Suh E, (2010) G-SQZ: compact encoding of genomic sequence and quality data. Bioin- formatics 26: 2192-2194.
11. Kozanitis C, Saunders C, Kruglyak S, Bafna V, Varghese G, (2010) Compressing genomic sequence fragments using SlimGene. Journal of Computational Biology 18: 401-413.
12. Jeon YJ, Park SH, Ahn SM, Hwang HJ, (2011) SOLiDzipper: A high speed encoding method for the next-generation sequencing data. Evol Bioinform Online 7: 1-6.
13. Deorowicz S, Grabowski S, (2011) Compression of DNA sequence reads in FASTQ format. Bioinformatics 27: 860-862.
14. Jones DC, Ruzzo WL, Peng X, Katze MG (2012) Compression of next-generation sequencing reads aided by highly efficient de novo assembly. Nucleic Acids Research in press.
15. Hach F, Numanagic I, Alkan C, Sahinalp SC (2012) SCALCE: boosting sequence compression algorithms using locally consistent encoding. Bioinformatics.
16. Grassi E (2012) KungFQ: A simple and powerful approach to compress fastq files. IEEE/ACM Transactions on Computational Biology and Bioinformatics in press.
17. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, et al. (2009) The Sequence Alignment/Map format and SAMtools. Bioinformatics 16: 2078-2079.
18. Fritz MHY, Leinonen R, Cochrane G, Birney E, (2011) Efficient storage of high throughput dna sequencing data using reference-based compression. Genome Research 21: 734-740.
19. Sakib MN, Tang J, Zheng WJ, Huang CT, (2011) Improving transmission efficiency of large Sequence Alignment/Map (SAM) files. PLoS ONE 6: e28251.
20. Popitsch N, von Haeseler A (2012) NGC: lossless and lossy compression of aligned high-throughput sequencing data. Nucl Acids Res.
21. Giancarlo R, Scaturro D, Utro F, (2009) Textual data compression in computational biology: a synopsis. Bioinformatics 25: 1575-1586.
22. Daily K, Rigor P, Christley S, Xie X, Baldi P (2010) Data structures and compression algorithms for high-throughput sequencing technologies. BMC Bioinformatics 11.
23. Deutsch P, Gailly JL (1996) Zlib compressed data format specification version 3.3. RFC 1950. Available: http://www.ietf.org/rfc/rfc1950.txt.
24. Kolmogorov A, (1968) Logical basis for information theory and probability theory. IEEE Transactions on Information Theory 14: 662-664.
25. The 1000 Genomes Consortium (2010) A map of human genome variation from population-scale sequencing. Nature 467: 1061-1073.
26. Ewing B, Green P, (1998) Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res 8: 186-194.
27. Witten IH, Neal RM, Cleary JG, (1987) Arithmetic coding for data compression. Commun ACM 30: 520-540.
28. Shannon C, Weaver W (1949) The mathematical theory of communication. Urbana: University of Illinois Press.
29. Minoche AE, Dohm JC, Himmelbauer H, (2011) Evaluation of genomic high-throughput sequencing data generated on illumina hiseq and genome analyzer systems. Genome Biology 12: R112.
30. Mahoney M (2005) Adaptive weighing of context models for lossless data compression. Technical Report CS-2005-16. Available: http://cs.fit.edu/~mmahoney/compression/cs200516.pdf.
31. Ziv J, Lempel A (1978) Compression of individual sequences via variable-rate coding. IEEE Transactions on information theory IT-24.
32. Li H, Durbin R, (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25: 1754-1760.
33. Langmead B, (2010) Aligning short sequencing reads with bowtie. Current Protocols in Bioinformatics 32: 11.7.1-11.7.14.