Aleksey V. Zimin | Searcharxiv

arXiv2013

A hierarchical network heuristic for solving the orientation problem in genome assembly

In the past several years, the problem of genome assembly has received considerable attention from both biologists and computer scientists. An important component of current assembly methods is the scaffolding process. This process involves building ordered and oriented linear collections of contigs (continuous overlapping sequence reads) called scaffolds and relies on the use of mate pair data. A mate pair is a set of two reads that are sequenced from the ends of a single fragment of DNA, and therefore have opposite mutual orientations. When two reads of a mate-pair are placed into two different contigs, one can infer the mutual orientation of these contigs. While several orientation algorithms exist as part of assembly programs, all encounter challenges while solving the orientation problem due to errors from mis-assemblies in contigs or errors in read placements. In this paper we present an algorithm based on hierarchical clustering that independently solves the orientation problem and is robust to errors. We show that our algorithm can correctly solve the orientation problem for both faux (generated) assembly data and real assembly data for {\em R. sphaeroides bacteria}. We demonstrate that our algorithm is stable to both changes in the initial orientations as well as noise in the data, making it advantageous compared to traditional approaches.

q-bio.GN↗

arXiv2003

A Local Ensemble Kalman Filter for Atmospheric Data Assimilation

In this paper, we introduce a new, local formulation of the ensemble Kalman Filter approach for atmospheric data assimilation. Our scheme is based on the hypothesis that, when the Earth's surface is divided up into local regions of moderate size, vectors of the forecast uncertainties in such regions tend to lie in a subspace of much lower dimension than that of the full atmospheric state vector of such a region. Ensemble Kalman Filters, in general, assume that the analysis resulting from the data assimilation lies in the same subspace as the expected forecast error. Under our hypothesis the dimension of this subspace is low. This implies that operations only on relatively low dimensional matrices are required. Thus, the data analysis is done locally in a manner allowing massively parallel computation to be exploited. The local analyses are then used to construct global states for advancement to the next forecast time. The method, its potential advantages, properties, and implementation requirements are illustrated by numerical experiments on the Lorenz-96 model. It is found that accurate analysis can be achieved at a cost which is very modest compared to that of a full global ensemble Kalman Filter.

physics.ao-ph↗