Improving transmission efficiency of large sequence alignment/map (SAM) files

PLoS ONE

Volumn 6, Issue 12, 2011, Pages

  Sakib, Muhammad Nazmus ^a   Tang, Jijun ^a   Zheng, W Jim ^b   Huang, Chin Tser ^a  

^a University of South Carolina   (United States)

^b MEDICAL UNIVERSITY OF SOUTH CAROLINA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ACCESS TO INFORMATION; ARTICLE; BITWISE FLAG; CONTROLLED STUDY; EXTENDED CIGAR; GENE SEQUENCE; INFORMATION PROCESSING; INSERT SIZE; MAPPING QUALITY; MATE POSITION; MATE REFERENCE NAME; ONLINE SYSTEM; POSITION OF CLIPPED ALIGNMENT; QUERY NAME; QUERY QUALITY; QUERY SEQUENCE; REFERENCE SEQUENCE NAME; SEQUENCE ALIGNMENT; SEQUENCE DATABASE; TIME; ALGORITHM; BIOLOGY; COMPUTER; COMPUTER LANGUAGE; COMPUTER NETWORK; COMPUTER PROGRAM; DNA SEQUENCE; GENOMICS; METHODOLOGY;

ALGORITHMS; COMPUTATIONAL BIOLOGY; COMPUTER COMMUNICATION NETWORKS; COMPUTERS; DATA COMPRESSION; GENOMICS; PROGRAMMING LANGUAGES; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA; SOFTWARE; TIME FACTORS;

EID: 82555175823     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0028251     Document Type: Article

References (5)

1. SAM Format Specification, Version 0.1.2-draft, August 20, 2009.
2. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, et al. (2009) The Sequence alignment/map (SAM) format and SAMtools. Bioinformatics 25 (16): 2078-9.
3. Kozanitis C, Saunders C, Kruglyak S, Bafna V, Varghese G, (2010) Compressing Genomic Sequence Fragments Using SLIMGENE. J Comput Biol 18 (3): 401-13.
4. Deorowicz S, Grabowski S, (2011) Compression of genomic sequences in FASTQ format. Bioinformatics 27 (6): 860-2.
5. Wang C, Zhang D, (2011) A novel compression tool for efficient storage of genome resequencing data. Nucl Acids Res 39 (7): e45.