Strand-seq enables reliable separation of long reads by chromosome via expectation maximization.
Strand-seq enables reliable separation of long reads by chromosome via expectation maximization.
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DOI：
10.1093/bioinformatics/bty290
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发表时间：
2018-07-01
期刊：
影响因子：
--
通讯作者：
Marschall T
中科院分区：
文献类型：
--
作者：
Ghareghani M;Porubskỳ D;Sanders AD;Meiers S;Eichler EE;Korbel JO;Marschall T
Current sequencing technologies are able to produce reads orders of magnitude longer than ever possible before. Such long reads have sparked a new interest in de novo genome assembly, which removes reference biases inherent to re-sequencing approaches and allows for a direct characterization of complex genomic variants. However, even with latest algorithmic advances, assembling a mammalian genome from long error-prone reads incurs a significant computational burden and does not preclude occasional misassemblies. Both problems could potentially be mitigated if assembly could commence for each chromosome separately. To address this, we show how single-cell template strand sequencing (Strand-seq) data can be leveraged for this purpose. We introduce a novel latent variable model and a corresponding Expectation Maximization algorithm, termed SaaRclust, and demonstrates its ability to reliably cluster long reads by chromosome. For each long read, this approach produces a posterior probability distribution over all chromosomes of origin and read directionalities. In this way, it allows to assess the amount of uncertainty inherent to sparse Strand-seq data on the level of individual reads. Among the reads that our algorithm confidently assigns to a chromosome, we observed more than 99% correct assignments on a subset of Pacific Bioscience reads with 30.1× coverage. To our knowledge, SaaRclust is the first approach for the in silico separation of long reads by chromosome prior to assembly. https://github.com/daewoooo/SaaRclust
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影响因子：
5.8
作者：
O'Neill, Kieran;Hills, Mark;Lansdorp, Peter M.
通讯作者：
Lansdorp, Peter M.
影响因子：
7
作者：
Sanders AD;Hills M;Porubský D;Guryev V;Falconer E;Lansdorp PM
通讯作者：
Lansdorp PM
影响因子：
7
作者：
Porubský D;Sanders AD;van Wietmarschen N;Falconer E;Hills M;Spierings DC;Bevova MR;Guryev V;Lansdorp PM
通讯作者：
Lansdorp PM
DOI：
10.1126/science.aae0344
发表时间：
2016-04-01
期刊：
Science (New York, N.Y.)
影响因子：
--
作者：
Gordon D;Huddleston J;Chaisson MJ;Hill CM;Kronenberg ZN;Munson KM;Malig M;Raja A;Fiddes I;Hillier LW;Dunn C;Baker C;Armstrong J;Diekhans M;Paten B;Shendure J;Wilson RK;Haussler D;Chin CS;Eichler EE
通讯作者：
Eichler EE
影响因子：
7.7
作者：
Claussin C;Porubský D;Spierings DC;Halsema N;Rentas S;Guryev V;Lansdorp PM;Chang M
通讯作者：
Chang M