Compression of structured high-throughput sequencing data

PLoS ONE

Volumn 8, Issue 11, 2013, Pages

  Campagne, Fabien ^a   Dorff, Kevin C ^a   Chambwe, Nyasha ^a   Robinson, James T ^b   Mesirov, Jill P ^b  

^a WEILL CORNELL MEDICAL COLLEGE   (United States)

^b MASSACHUSETTS INSTITUTE OF TECHNOLOGY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

COMPUTATIONAL BIOLOGY; DATA COMPRESSION; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; SOFTWARE;

EID: 84894193223     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0079871     Document Type: Article

References (21)

1. Mangone M, Manoharan AP, Thierry-Mieg D, Thierry-Mieg J, Han T, et al. (2010) The landscape of C. elegans 3'UTRs. Science 329: 432-435.
2. Agrawal N, Frederick MJ, Pickering CR, Bettegowda C, Chang K, et al. (2011) Exome sequencing of head and neck squamous cell carcinoma reveals inactivating mutations in NOTCH1. Science 333: 1154-1157.
3. Shearstone JR, Pop R, Bock C, Boyle P, Meissner A, et al. (2011) Global DNA demethylation during mouse erythropoiesis in vivo. Science 334: 799-802.
4. Mardis ER (2011) A decade's perspective on DNA sequencing technology. Nature 470: 198-203.
5. Cock PJ, Fields CJ, Goto N, Heuer ML, Rice PM The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants. Nucleic Acids Res 38: 1767-1771.
6. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, et al. (2009) The Sequence Alignment/Map format and SAMtools. Bioinformatics 25: 2078-2079.
7. Hsi-Yang Fritz M, Leinonen R, Cochrane G, Birney E (2011) Efficient storage of high throughput DNA sequencing data using reference-based compression. Genome Res 21: 734-740.
8. Robinson JT, Thorvaldsdottir H, Winckler W, Guttman M, Lander ES, et al. (2011) Integrative genomics viewer. Nat Biotechnol 29: 24-26.
9. Li H, Durbin R (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25: 1754-1760.
10. Wu TD, Nacu S (2010) Fast and SNP-tolerant detection of complex variants and splicing in short reads. Bioinformatics 26: 873-881.
11. Varda K (2008) Protocol Buffers. Available: http://code.google.com/p/ protobuf/.
12. Campagne F, Dorff K, Chambwe N, Robinson JT, Mesirov JP, et al. (2012) Compression of structured high-throughput sequencing data. Preprint at arXiv. Available: http://arxiv.org/abs/1211.6664.
13. Burrows M WD (1994) A block-sorting lossless data compression algorithm. Digital Equipment Corporation.
14. Effros M. PPM Performance with BWT Complexity: A Fast and Effective Data Compression Algorithm; 2000; Washington, DC, USA.
15. Popitsch N, von Haeseler A (2012) NGC: lossless and lossy compression of aligned high-throughput sequencing data. Nucleic Acids Res 41: e27.
16. (2012) Sequence Squeeze Competition. Available: http://www. sequencesqueeze.org/.
17. Dorff KC, Chambwe N, Zeno Z, Shaknovich R, Campagne F (2012) GobyWeb: simplified management and analysis of gene expression and DNA methylation sequencing data. arXiv http://arxivorg/abs/12116666.
18. Kielbasa SM, Wan R, Sato K, Horton P, Frith MC (2011) Adaptive seeds tame genomic sequence comparison. Genome Res 21: 487-493.
19. Skrabanek L, Murcia M, Bouvier M, Devi L, George SR, et al. (2007) Requirements and ontology for a G protein-coupled receptor oligomerization knowledge base. BMC bioinformatics 8: 177.
20. Boldi P, Vigna S. MG4J at TREC 2005. In: Buckland EMVaLP, editor. Special Publications; 2005. NIST.
21. Pickrell JK, Marioni JC, Pai AA, Degner JF, Engelhardt BE, et al. (2010) Understanding mechanisms underlying human gene expression variation with RNA sequencing. Nature 464: 768-772.