Abstract
Environmental and clinical settings can host a wide variety of both bacterial species and strains in a single colony but accurate identification of the organisms is difficult. We describe BIB, a probabilistic method for estimating the relative abundances of species or strains contained in mixed samples analyzed by short read high-throughput sequencing. By grouping closely related strains together in clusters, the BIB pipeline is capable of estimating the relative abundances of the clusters contained in a sequencing sample.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Balmer O, Tanner M (2011) Prevalence and implications of multiple-strain infections. Lancet Infect Dis 11:868–878
Didelot X, Bowden R, Wilson DJ, Peto TEA, Crook DW (2012) Transforming clinical microbiology with bacterial genome sequencing. Nat Rev Genet 13:601–612
Brito IL, Alm EJ (2016) Tracking strains in the microbiome: insights from metagenomics and models. Front Microbiol 7:712
Breitwieser FP, Lu J, Salzberg SL (2017) A review of methods and databases for metagenomic classification and assembly. Brief Bioinf https://doi.org/10.1093/bib/bbx120
Sankar A, Malone B, Bayliss SC, Pascoe B, MĂ©ric G, Hitchings MD et al (2016) Bayesian identification of bacterial strains from sequencing data. Microb Genomics 2:e000075
Glaus P, Honkela A, Rattray M (2012) Identifying differentially expressed transcripts from RNA-seq data with biological variation. Bioinformatics 28:1721–1728
Hensman J, Papastamoulis P, Glaus P, Honkela A, Rattray M (2015) Fast and accurate approximate inference of transcript expression from RNA-seq data. Bioinformatics 31:3881–3889
Kanitz A, Gypas F, Gruber AJ, Gruber AR, Martin G, Zavolan M (2015) Comparative assessment of methods for the computational inference of transcript isoform abundance from RNA-seq data. Genome Biol 16:150
Xing Y, Yu T, Wu YN, Roy M, Kim J, Lee C (2006) An expectation-maximization algorithm for probabilistic reconstructions of full-length isoforms from splice graphs. Nucleic Acids Res 34:3150–3160
Jiang H, Wong WH (2009) Statistical inferences for isoform expression in RNA-Seq. Bioinformatics 25:1026–1032
Li B, Ruotti V, Stewart RM, Thomson JA, Dewey CN (2010) RNA-Seq gene expression estimation with read mapping uncertainty. Bioinformatics 26:493–500
Maiden MC, Bygraves JA, Feil E, Morelli G, Russell JE, Urwin R et al (1998) Multilocus sequence typing: a portable approach to the identification of clones within populations of pathogenic microorganisms. Proc Natl Acad Sci USA 95:3140–3145
Cheng L, Connor TR, Sirén J, Aanensen DM, Corander J (2013) Hierarchical and spatially explicit clustering of DNA sequences with BAPS software. Mol Biol Evol 30:1224–1228
Corander J, Sirén J, Arjas E (2008) Bayesian spatial modeling of genetic population structure. Comput Stat 23:111
Langmead B, Salzberg SL (2012) Fast gapped-read alignment with Bowtie 2. Nat Methods 9:357–359
Acknowledgements
This work was supported by the Academy of Finland [259440 to A.H., 251170 to J.C.].
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2018 Springer Science+Business Media, LLC, part of Springer Nature
About this protocol
Cite this protocol
Mäklin, T., Corander, J., Honkela, A. (2018). Identifying Bacterial Strains from Sequencing Data. In: Mamitsuka, H. (eds) Data Mining for Systems Biology. Methods in Molecular Biology, vol 1807. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-8561-6_1
Download citation
DOI: https://doi.org/10.1007/978-1-4939-8561-6_1
Published:
Publisher Name: Humana Press, New York, NY
Print ISBN: 978-1-4939-8560-9
Online ISBN: 978-1-4939-8561-6
eBook Packages: Springer Protocols