Contig assembly is the first stage that most assemblers solve when reconstructing a genome from a set of reads. Its output consists of contigs -- a set of strings that are promised to appear in any genome that could have generated the reads. From the introduction of contigs 20 years ago, assemblers have tried to obtain longer and longer contigs, but the following question was never solved: given a genome graph @math (e.g. a de Bruijn, or a string graph), what are all the strings that can be safely reported from @math as contigs? In this paper we finally answer this question, and also give a polynomial time algorithm to find them. Our experiments show that these strings, which we call omnitigs, are 66 to 82 longer on average than the popular unitigs, and 29 of dbSNP locations have more neighbors in omnitigs than in unitigs.
There are a few notable exceptions. @cite_26 , Boisvert and colleagues also define the assembly problem in terms of finding contigs, rather than a single reconstruction. Nagarajan and Pop @cite_31 observe that Waterman's characterization @cite_13 of the graphs with a unique Eulerian tour leads to a simple algorithm for finding all safe strings when a genomic reconstruction is an Eulerian tour. They also suggest an approach for finding all the safe strings when a genomic reconstruction is a Chinese Postman tour @cite_31 . We note, however, that in the Eulerian model, the exact copy count of each edge should be known in advance, while in the Chinese Postman model (minimizing the length of the genomic reconstruction), the solution will over-collapse all tandem repeats. Furthermore, these approaches have not been implemented and hence their effectiveness is unknown.
@cite_31 @cite_26 @cite_13
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Consider a Markov chain on an infinite tree T = (V,E) rooted at . In such a chain, once the initial root state ( ) is chosen, each vertex iteratively chooses its state from the one of its parent by an application of a Markov transition rule (and all such applications are independent). Let µj denote the resulting measure for ( ) = j. µj is defined on configurations = ( (x))x2V 2 A V , where A is some finite set. Let µ n denote the restriction of µ to the sigma-algebra generated by the variables (x) where x is at distance exactly n from . Letting n = maxi,j2A dTV (µ n ,µ n ), where dTV denotes total variation distance, we say that the reconstruction problem is solvable if liminfn!1 n > 0. Reconstruction solvability roughly means that the n’th level of the tree contains a non-vanishing amount of information on the root of the tree, as n ! 1. In this paper we study the problem of robust reconstruction. Let be a non degenerate distribution on A and > 0. Let be chosen according to µ n and 0 be obtained from by letting for each node independently (v) = 0 (v) with probability 1 and 0 (v) to be an independent sample from otherwise. We denote by µ n [, ] the resulting measure on 0 . The measure µ n [, ] is a perturbation of the measure µ n . Letting n(, ) = maxi,j2A dTV (µ n [, ],µ n [, ]), we say that the reconstruction problem is -robust-solvable if liminfn!1 n(, ) > 0 for all 0 1, where 2(M) is the second largest eigenvalue of M (in absolute value), then for all non-degenerate , the reconstruction problem is -robust-solvable. We prove a converse and show that the reconstruction problem is not -robust-solvable if B| 2(M)| 2 < 1. This proves a conjecture by the second author and Peres. We also consider other models of noise and general trees. The emergence of next-generation sequencing platforms led to resurgence of research in whole-genome shotgun assembly algorithms and software. DNA sequencing data from the Roche 454, Illumina Solexa, and ABI SOLiD platforms typically present shorter read lengths, higher coverage, and different error profiles compared with Sanger sequencing data. Since 2005, several assembly software packages have been created or revised specifically for de novo assembly of next-generation sequencing data. This review summarizes and compares the published descriptions of packages named SSAKE, SHARCGS, VCAKE, Newbler, Celera Assembler, Euler, Velvet, ABySS, AllPaths, and SOAPdenovo. More generally, it compares the two standard methods known as the de Bruijn graph approach and the overlap layout consensus approach to assembly. Restoration of writing order from a single-stroked handwriting image can be seen as the problem of finding the smoothest path in its graph representation. In this paper, a 3-phase approach to restore a writing order is proposed within the framework of the edge continuity relation (ECR). In the initial, local phase, in order to obtain possible ECRs at an even-degree node, a neural network is used for the node of degree 4 and a theoretical approach is presented for the node of degree higher than 4 by introducing certain reasonable assumptions. In the second phase, we identify double-traced lines by employing maximum weighted matching. This makes it possible to transform the problem of obtaining possible ECRs at odd-degree node to that at even-degree node. In the final, global phase, we find all the candidates of single-stroked paths by depth first search and select the best one by evaluating SLALOM smoothness. Experiments on static images converted from online data in the Unipen database show that our method achieves a restoration rate of 96.0 percent We consider homogeneous factor models on uniformly sparse graph sequences converging locally to a (unimodular) random tree T, and study the existence of the free energy density ϕ, the limit of the log-partition function divided by the number of vertices n as n tends to infinity. We provide a new interpolation scheme and use it to prove existence of, and to explicitly compute, the quantity ϕ subject to uniqueness of a relevant Gibbs measure for the factor model on T. By way of example we compute ϕ for the independent set (or hard-core) model at low fugacity, for the ferromagnetic Ising model at all parameter values, and for the ferromagnetic Potts model with both weak enough and strong enough interactions. Even beyond uniqueness regimes our interpolation provides useful explicit bounds on ϕ. In the regimes in which we establish existence of the limit, we show that it coincides with the Bethe free energy functional evaluated at a suitable fixed point of the belief propagation (Bethe) recursions on T. In the special case that T has a Galton–Watson law, this formula coincides with the nonrigorous “Bethe prediction” obtained by statistical physicists using the “replica” or “cavity” methods. Thus our work is a rigorous generalization of these heuristic calculations to the broader class of sparse graph sequences converging locally to trees. We also provide a variational characterization for the Bethe prediction in this general setting, which is of independent interest.