Motivation: The enormous amount of short reads generated by the new DNA sequencing technologies call for the development of fast and accurate read alignment programs. A first generation of hash table-based methods has been developed, including MAQ, which is accurate, feature rich and fast enough to align short reads from a single individual. However, MAQ does not support gapped alignment for single-end reads, which makes it unsuitable for alignment of longer reads where indels may occur frequently. The speed of MAQ is also a concern when the alignment is scaled up to the resequencing of hundreds of individuals.

Results: We implemented Burrows-Wheeler Alignment tool (BWA), a new read alignment package that is based on backward search with Burrows–Wheeler Transform (BWT), to efficiently align short sequencing reads against a large reference sequence such as the human genome, allowing mismatches and gaps. BWA supports both base space reads, e.g. from Illumina sequencing machines, and color space reads from AB SOLiD machines. Evaluations on both simulated and real data suggest that BWA is ~10–20× faster than MAQ, while achieving similar accuracy. In addition, BWA outputs alignment in the new standard SAM (Sequence Alignment/Map) format. Variant calling and other downstream analyses after the alignment can be achieved with the open source SAMtools software package.

Availability: http://maq.sourceforge.net 

Contact: [email protected]

/pdf/fast-and-accurate-short-read-alignment-with-burrows-wheeler-43uqhgr33c.pdf

Fast and accurate short read alignment with Burrows–Wheeler transform

We survey the current techniques to cope with the problem of string matching that allows errors. This is becoming a more and more relevant issue for many fast growing areas such as information retrieval and computational biology. We focus on online searching and mostly on edit distance, explaining the problem and its relevance, its statistical behavior, its history and current developments, and the central ideas of the algorithms and their complexities. We present a number of experiments to compare the performance of the different algorithms and show which are the best choices. We conclude with some directions for future work and open problems.

/pdf/a-guided-tour-to-approximate-string-matching-22fowlmq5b.pdf

A guided tour to approximate string matching

An edited volume containing data structures and algorithms for information retrieved including a disk with examples written in C. For programmers and students interested in parsing text, automated indexing, its the first collection in book form of the basic data structures and algorithms that are critical to the storage and retrieval of documents.

https://hornad.fei.tuke.sk/~genci/Vyucba/OOBDS/Archiv/Podklady/TExtoveIS&IR/Information%20Retrieval%20Data%20Structures%20&%20Algorithms.PDF

Information Retrieval: Data Structures and Algorithms

An on-line algorithm is presented for constructing the suffix tree for a given string in time linear in the length of the string. The new algorithm has the desirable property of processing the string symbol by symbol from left to right. It always has the suffix tree for the scanned part of the string ready. The method is developed as a linear-time version of a very simple algorithm for (quadratic size) suffixtries. Regardless of its quadratic worst case this latter algorithm can be a good practical method when the string is not too long. Another variation of this method is shown to give, in a natural way, the well-known algorithms for constructing suffix automata (DAWGs).

https://web.stanford.edu/~mjkay/Ukkonen.pdf

On-line construction of suffix trees

Rapidly evolving sequencing technologies produce data on an unparalleled scale. A central challenge to the analysis of this data is sequence alignment, whereby sequence reads must be compared to a reference. A wide variety of alignment algorithms and software have been subsequently developed over the past two years. In this article, we will systematically review the current development of these algorithms and introduce their practical applications on different types of experimental data. We come to the conclusion that short-read alignment is no longer the bottleneck of data analyses. We also consider future development of alignment algorithms with respect to emerging long sequence reads and the prospect of cloud computing.

/pdf/a-survey-of-sequence-alignment-algorithms-for-next-3a60i3hz3r.pdf

A survey of sequence alignment algorithms for next-generation sequencing.

The smallest automaton recognizing the subwords of a text

A clean version of Weiner’s linear-time compact-subword-tree construction simultaneously also constructs the smallest deterministic finite automaton recognizing the reverse subwords.

/pdf/efficient-and-elegant-subword-tree-construction-19ggyj5p46.pdf

Efficient and Elegant Subword-Tree Construction

By means of numerical simulation and experimental, the liquid filling forming process of an aluminum alloy double concave and convex curved sheet part was studied. The quality of forming parts, especially the thinning rate, is compared and studied during different hydroforming process. The results show that the thinning rate of the product is more than 25% regardless of the passive or active liquid filling drawing. However, the maximum thinning rate of the product is less than 20% when the hybrid hydroforming is carried out in a set of die with passive liquid filling in sequence, followed by pulsating reverse liquid filling. The method has reference significance for improving the forming quality of the parts with concave and convex surface of thin plate.

Study on hybrid hydroforming process of sheet metal with multi-concave and convex surface parts

In this work, a variable thickness tube blank geometry is proposed to be used in T-shaped tube hydroforming. The dimensions of the tube blank are optimized by the response surface method (RSM) linked with finite element simulation during T-shaped tube hydroforming. The influence of the wall thickness, angle and length of the tube blank are discussed on the thinning ratio and branch height. Multi-objective functions that relate objectives and design variables are formulated. Furthermore, the design variables having greatest impact on the objectives are obtained by sensitivity analysis. The optimal the geometric dimensions are determined within the given criterion by RSW and desirability approach. The optimized results have good agreement with the obtained results by finite element simulation and experiment.

M. T. Chen

Papers

The smallest automaton recognizing the subwords of a text

Efficient and Elegant Subword-Tree Construction

Study on hybrid hydroforming process of sheet metal with multi-concave and convex surface parts

Dimensional optimization of variable thickness tube in T-shaped tube hydroforming using response surface methodology