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231225s2018 xx |||||o 00| ||eng c |
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|a 10.1080/02664763.2018.1426741
|2 doi
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|a eng
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| 100 |
1 |
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|a Du, Ruofei
|e verfasserin
|4 aut
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| 245 |
1 |
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|a Statistical correction for functional metagenomic profiling of a microbial community with short NGS reads
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|c 2018
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|a Text
|b txt
|2 rdacontent
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|a ƒaComputermedien
|b c
|2 rdamedia
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| 338 |
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|a ƒa Online-Ressource
|b cr
|2 rdacarrier
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| 500 |
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|a Date Revised 20.11.2019
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|a published: Print-Electronic
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|a Citation Status PubMed-not-MEDLINE
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|a By sequence homology search, the list of all the functions found and the counts of reads being aligned to them present the functional profile of a metagenomic sample. However, a significant obstacle has been observed in this approach due to the short read length associated with many next generation sequencing technologies. This includes artificial families, cross-annotations, length bias and conservation bias. The widely applied cutoff methods, such as BLAST E-value, are not able to solve the problems. Following the published successful procedures on the artificial families and the cross-annotation issue, we propose in this paper to use zero-truncated Poisson and Binomial (ZTP-Bin) hierarchical modelling to correct the length bias and the conservation bias. Goodness-of-fit of the modelling and cross-validation for the prediction using a bioinformatic simulated sample show the validity of this approach. Evaluated on an in vitro-simulated data set, the proposed modelling method outperforms other traditional methods. All three steps were then sequentially applied on real-life metagenomic samples to show that the proposed framework will lead to a more accurate functional profile of a short read metagenomic sample
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|a Journal Article
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|a Primary 62F10
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| 650 |
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4 |
|a conservation bias
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| 650 |
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4 |
|a functional profiling
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| 650 |
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4 |
|a length bias
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| 650 |
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4 |
|a metagenomics
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| 650 |
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4 |
|a secondary 62P10
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| 650 |
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4 |
|a short reads
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| 700 |
1 |
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|a Fang, Zhide
|e verfasserin
|4 aut
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| 773 |
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|i Enthalten in
|t Journal of applied statistics
|d 1991
|g 45(2018), 14 vom: 01., Seite 2521-2535
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|x 0266-4763
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| 773 |
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|g volume:45
|g year:2018
|g number:14
|g day:01
|g pages:2521-2535
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| 856 |
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|u http://dx.doi.org/10.1080/02664763.2018.1426741
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