Dominique Lavenier

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Low-cost short read sequencing technology has revolutionized genomics, though it is only just becoming practical for the high-quality de novo assembly of a novel large genome. We describe the Assemblathon 1 competition, which aimed to comprehensively assess the state of the art in de novo assembly methods when applied to current sequencing technologies. In(More)
BACKGROUND The process of generating raw genome sequence data continues to become cheaper, faster, and more accurate. However, assembly of such data into high-quality, finished genome sequences remains challenging. Many genome assembly tools are available, but they differ greatly in terms of their performance (speed, scalability, hardware requirements,(More)
The Streams-C compiler ([5]) synthesizes hardware circuits for reconfigurable FPGA-based computers from parallel C programs. The Streams-C language consists of a small number of libraries and intrinsic functions added to a synthesizable subset of C, and supports a communicating process programming model. The processes may be either software or hardware(More)
SUMMARY Counting all the k-mers (substrings of length k) in DNA/RNA sequencing reads is the preliminary step of many bioinformatics applications. However, state of the art k-mer counting methods require that a large data structure resides in memory. Such structure typically grows with the number of distinct k-mers to count. We present a new streaming(More)
MOTIVATION SAMBA (Systolic Accelerator for Molecular Biological Applications) is a 128 processor hardware accelerator for speeding up the sequence comparison process. The short-term objective is to provide a low-cost board to boost PC or workstation performance on this class of applications. This paper places SAMBA amongst other existing systems and(More)
Graphical representation of DNA sequences provides a simple and intuitive way of viewing, anchoring, and comparing various gene structures, so a simple and non-degenerate method is attractive to both biologists and computational biologists. In this study, a universal graphical representation method for DNA sequences based on S.S.-T. Yau's method is(More)
The Pixel Purity Index (PPI) algorithm is used as a pre-processing to find end-members in a hyper spectral image. It tries to identify pure spectra by assigning a pixel purity index to each pixel in the image. The algorithm proceeds by generating a large number of random vectors through the hyper spectral image and by computing a dot-product between each(More)