Optimizing read mapping to reference genomes to determine composition and species prevalence in microbial communities

PLoS ONE

Volumn 7, Issue 6, 2012, Pages

  Martin, John ^a   Sykes, Sean ^b   Young, Sarah ^b   Kota, Karthik ^a   Sanka, Ravi ^c   Sheth, Nihar ^d   Orvis, Joshua ^e   Sodergren, Erica ^a   Wang, Zhengyuan ^a   Weinstock, George M ^a   Mitreva, Makedonka ^a  

^a WASHINGTON UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b BROAD INSTITUTE OF MIT AND HARVARD   (United States)

^c J CRAIG VENTER INSTITUTE   (United States)

^d VIRGINIA COMMONWEALTH UNIVERSITY   (United States)

^e UNIVERSITY OF MARYLAND SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BACTERIAL GENOME; BODY REGIONS; CONTROLLED STUDY; DATA ANALYSIS; DATA BASE; GENE MAPPING; GENE SEQUENCE; GENETIC SIMILARITY; HUMAN MICROBIOME PROJECT; METAGENOMICS; MICROBIAL COMMUNITY; MICROBIOME; NONHUMAN; PHYLOGENY; SENSITIVITY AND SPECIFICITY; SEQUENCE ALIGNMENT; SPECIES COMPOSITION; TAXONOMY;

BIODIVERSITY; DATABASES, FACTUAL; HUMANS; METAGENOME; METAGENOMICS; PHYLOGENY;

EID: 84862189439     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0036427     Document Type: Article

References (27)

1. Peterson J, Garges S, Giovanni M, McInnes P, Wang L, (2009) The NIH Human Microbiome Project. Genome Res 19: 2317 2323.
2. Handelsman J, (2004) Metagenomics: application of genomics to uncultured microorganisms. Microbiol Mol Biol Rev 68: 669 685.
3. Riesenfeld CS, Goodman RM, Handelsman J, (2004) Uncultured soil bacteria are a reservoir of new antibiotic resistance genes. Environ Microbiol 6: 981 989.
4. Kumar Y, Westram R, Kipfer P, Meier H, Ludwig W, (2006) Evaluation of sequence alignments and oligonucleotide probes with respect to three-dimensional structure of ribosomal RNA using ARB software package. BMC Bioinformatics 7: 240.
5. DeSantis TZ Jr, Hugenholtz P, Keller K, Brodie EL, Larsen N, (2006) NAST: a multiple sequence alignment server for comparative analysis of 16S rRNA genes. Nucleic Acids Res 34: W394 399.
6. Schloss PD, Westcott SL, (2011) Assessing and Improving Methods Used in Operational Taxonomic Unit-Based Approaches for 16S rRNA Gene Sequence Analysis. Appl Environ Microbiol 77: 3219 3226.
7. Li H, Homer N, (2010) A survey of sequence alignment algorithms for next-generation sequencing. Brief Bioinform 11: 473 483.
8. Eckburg PB, Bik EM, Bernstein CN, Purdom E, Dethlefsen L, (2005) Diversity of the human intestinal microbial flora. Science 308: 1635 1638.
9. Li H, Durbin R, (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25: 1754 1760.
10. Li R, Yu C, Li Y, Lam TW, Yiu SM, (2009) SOAP2: an improved ultrafast tool for short read alignment. Bioinformatics 25: 1966 1967.
11. Hancock JM, Armstrong JS, (1994) SIMPLE34: an improved and enhanced implementation for VAX and Sun computers of the SIMPLE algorithm for analysis of clustered repetitive motifs in nucleotide sequences. Comput Appl Biosci 10: 67 70.
12. Makarova KS, Omelchenko MV, Gaidamakova EK, Matrosova VY, Vasilenko A, (2007) Deinococcus geothermalis: the pool of extreme radiation resistance genes shrinks. PLoS One 2: e955.
13. White O, Eisen JA, Heidelberg JF, Hickey EK, Peterson JD, (1999) Genome sequence of the radioresistant bacterium Deinococcus radiodurans R1. Science 286: 1571 1577.
14. Ajdic D, McShan WM, McLaughlin RE, Savic G, Chang J, (2002) Genome sequence of Streptococcus mutans UA159, a cariogenic dental pathogen. Proc Natl Acad Sci U S A 99: 14434 14439.
15. Tettelin H, Masignani V, Cieslewicz MJ, Eisen JA, Peterson S, (2002) Complete genome sequence and comparative genomic analysis of an emerging human pathogen, serotype V Streptococcus agalactiae. Proc Natl Acad Sci U S A 99: 12391 12396.
16. Tettelin H, Nelson KE, Paulsen IT, Eisen JA, Read TD, (2001) Complete genome sequence of a virulent isolate of Streptococcus pneumoniae. Science 293: 498 506.
17. Wang Q, Garrity GM, Tiedje JM, Cole JR, (2007) Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol 73: 5261 5267.
18. Rasko DA, Ravel J, Okstad OA, Helgason E, Cer RZ, (2004) The genome sequence of Bacillus cereus ATCC 10987 reveals metabolic adaptations and a large plasmid related to Bacillus anthracis pXO1. Nucleic Acids Res 32: 977 988.
19. Medini D, Donati C, Tettelin H, Masignani V, Rappuoli R, (2005) The microbial pan-genome. Curr Opin Genet Dev 15: 589 594.
20. Haas BJ, Gevers D, Earl AM, Feldgarden M, Ward DV, (2011) Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons. Genome Res 21: 494 504.
21. Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Sayers EW, (2011) GenBank. Nucleic Acids Res 39: D32 37.
22. Darling AC, Mau B, Blattner FR, Perna NT, (2004) Mauve: multiple alignment of conserved genomic sequence with rearrangements. Genome Res 14: 1394 1403.
23. CLCbio website. http://www.clcbio.com Accessed 2012 April 9.
24. Reumers J, De Rijk P, Zhao H, Liekens A, Smeets D, (2012) Optimized filtering reduces the error rate in detecting genomic variants by short-read sequencing. Nat Biotechnol 30: 61 68.
25. SMALT website. http://www.sanger.ac.uk/resources/software/smalt/ Accessed 2012 April 9.
26. Li H, Ruan J, Durbin R, (2008) Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Res 18: 1851 1858.
27. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, (2009) The Sequence Alignment/Map format and SAMtools. Bioinformatics 25: 2078 2079.