GPU-Accelerated BWT Construction for Large Collection of Short Reads

Advances in DNA sequencing technology have stimulated the development of algorithms and tools for processing very large collections of short strings (reads). Short-read alignment and assembly are among the most well-studied problems. Many state-of-the-art aligners, at their core, have used the Burrows-Wheeler transform (BWT) as a main-memory index of a reference genome (typical example, NCBI human genome). Recently, BWT has also found its use in string-graph assembly, for indexing the reads (i.e., raw data from DNA sequencers). In a typical data set, the volume of reads is tens of times of the sequenced genome and can be up to 100 Gigabases. Note that a reference genome is relatively stable and computing the index is not a frequent task. For reads, the index has to computed from scratch for each given input. The ability of efficient BWT construction becomes a much bigger concern than before. In this paper, we present a practical method called CX1 for constructing the BWT of very large string collections. CX1 is the first tool that can take advantage of the parallelism given by a graphics processing unit (GPU, a relative cheap device providing a thousand or more primitive cores), as well as simultaneously the parallelism from a multi-core CPU and more interestingly, from a cluster of GPU-enabled nodes. Using CX1, the BWT of a short-read collection of up to 100 Gigabases can be constructed in less than 2 hours using a machine equipped with a quad-core CPU and a GPU, or in about 43 minutes using a cluster with 4 such machines (the speedup is almost linear after excluding the first 16 minutes for loading the reads from the hard disk). The previously fastest tool BRC is measured to take 12 hours to process 100 Gigabases on one machine; it is non-trivial how BRC can be parallelized to take advantage a cluster of machines, let alone GPUs.Comment: 11 page

The Role of Indexing in Subject Retrieval

On first reading the list of speakers proposed for this institute, I became aware of being rather the "odd man out" for two reasons. Firstly, I was asked to present a paper on PRECIS which is very much a verbal indexing system-at a conference dominated by contributions on classification schemes with a natural bias, as the centenary year approaches, toward the Dewey Decimal Classification (DDC). Secondly, I feared (quite wrongly, as it happens) that I might be at variance with one or two of my fellow speakers, who would possibly like to assure us, in an age when we can no longer ignore the computer, that traditional library schemes such as DDC and Library of Congress Classification (LCC) are capable of maintaining their original function of organizing collections of documents, and at the same time are also well suited to the retrieval of relevant citations from machine-held files. In this context, I am reminded of a review of a general collection of essays on classification schemes which appeared in the Journal of Documentation in 1972. Norman Roberts, reviewing the papers which dealt specifically with the well established schemes, deduced that "all the writers project their particular schemes into the future with an optimism that springs, perhaps, as much from a sense of emotional involvement as from concrete evidence." Since I do not believe that these general schemes can play any significant part in the retrieval of items from mechanized files, it appeared that I had been cast in the role of devil's advocate.published or submitted for publicatio

Reify Your Collection Queries for Modularity and Speed!

Modularity and efficiency are often contradicting requirements, such that programers have to trade one for the other. We analyze this dilemma in the context of programs operating on collections. Performance-critical code using collections need often to be hand-optimized, leading to non-modular, brittle, and redundant code. In principle, this dilemma could be avoided by automatic collection-specific optimizations, such as fusion of collection traversals, usage of indexing, or reordering of filters. Unfortunately, it is not obvious how to encode such optimizations in terms of ordinary collection APIs, because the program operating on the collections is not reified and hence cannot be analyzed. We propose SQuOpt, the Scala Query Optimizer--a deep embedding of the Scala collections API that allows such analyses and optimizations to be defined and executed within Scala, without relying on external tools or compiler extensions. SQuOpt provides the same "look and feel" (syntax and static typing guarantees) as the standard collections API. We evaluate SQuOpt by re-implementing several code analyses of the Findbugs tool using SQuOpt, show average speedups of 12x with a maximum of 12800x and hence demonstrate that SQuOpt can reconcile modularity and efficiency in real-world applications.Comment: 20 page

Principles and Implementation of Deductive Parsing

We present a system for generating parsers based directly on the metaphor of parsing as deduction. Parsing algorithms can be represented directly as deduction systems, and a single deduction engine can interpret such deduction systems so as to implement the corresponding parser. The method generalizes easily to parsers for augmented phrase structure formalisms, such as definite-clause grammars and other logic grammar formalisms, and has been used for rapid prototyping of parsing algorithms for a variety of formalisms including variants of tree-adjoining grammars, categorial grammars, and lexicalized context-free grammars.Comment: 69 pages, includes full Prolog cod

Prospects and limitations of full-text index structures in genome analysis

The combination of incessant advances in sequencing technology producing large amounts of data and innovative bioinformatics approaches, designed to cope with this data flood, has led to new interesting results in the life sciences. Given the magnitude of sequence data to be processed, many bioinformatics tools rely on efficient solutions to a variety of complex string problems. These solutions include fast heuristic algorithms and advanced data structures, generally referred to as index structures. Although the importance of index structures is generally known to the bioinformatics community, the design and potency of these data structures, as well as their properties and limitations, are less understood. Moreover, the last decade has seen a boom in the number of variant index structures featuring complex and diverse memory-time trade-offs. This article brings a comprehensive state-of-the-art overview of the most popular index structures and their recently developed variants. Their features, interrelationships, the trade-offs they impose, but also their practical limitations, are explained and compared

Phonetic Searching

An improved method and apparatus is disclosed which uses probabilistic techniques to map an input search string with a prestored audio file, and recognize certain portions of a search string phonetically. An improved interface is disclosed which permits users to input search strings, linguistics, phonetics, or a combination of both, and also allows logic functions to be specified by indicating how far separated specific phonemes are in time.Georgia Tech Research Corporatio