Rapid identification of non-human sequences in high-throughput sequencing datasets

Bioinformatics

Volumn 28, Issue 8, 2012, Pages 1174-1175

  Bhaduri, Aparna ^a,b   Qu, Kun ^a,b   Lee, Carolyn S ^a,b   Ungewickell, Alexander ^a,b   Khavari, Paul A ^a,b  

^a VA PALO ALTO HEALTH CARE SYSTEM   (United States)

^b STANFORD UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CLASSIFICATION; COMPUTER PROGRAM; DNA SEQUENCE; GENETICS; GENOME; HIGH THROUGHPUT SEQUENCING; HOST PATHOGEN INTERACTION; HUMAN; HUMAN GENOME; ISOLATION AND PURIFICATION; VIRUS;

GENOME; GENOME, HUMAN; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HOST-PATHOGEN INTERACTIONS; HUMANS; SEQUENCE ANALYSIS, DNA; SOFTWARE; VIRUSES;

EID: 84859770226     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/bts100     Document Type: Note

References (10)

1. Benson, D.A. et al. (2008) GenBank. Nucl. Acids Res., 36, D25-D30.
2. Feng, H. et al. (2008) Clonal integration of a polyomavirus in human Merkel cell carcinoma. Science, 319, 1096-1100.
3. Grabherr, M.G. et al. (2011) Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat. Biotechnol., 29, 644-652.
4. Kent, W.J. (2002) BLAT-the BLAST-like alignment tool. Genome Res., 12, 656-664.
5. Kostic, A.D. et al. (2011) PathSeq: software to identify or discover microbes by deep sequencing of human tissue. Nat. Biotechnol., 29, 393-396.
6. Langmead, B. et al. (2009) Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol., 10, R25.
7. Prensner, J.R. et al. (2011) Transcriptome sequencing across a prostate cancer cohort identifies PCAT-1an unannotated lincRNA implicated in disease progression. Nat. Biotechnol., 29, 742-749.
8. Shendure, J. and H. Ji (2008) Next-generation DNA sequencing. Nat. Biotechnol., 26, 1135-1145.
9. Welch, T.A. (1984) A technique for high-performance data-compression. Computer, 17, 8-19.
10. Yozwiak, N.L. et al. (2010) Human enterovirus 109: a novel interspecies recombinant enterovirus isolated from a case of acute pediatric respiratory illness in Nicaragua. J. Virol., 84, 9047-9058.