NONLINEAR FM INDEX APPLICATION FOR ALIGNMENT OF SHORT DNA SEQUENCES USING RE-PARAMETRIZATION OF ALGORITHMS

An innovative reconfiguration application is proposed to re-calculate the parameters of the Ferragina and Manzini exact search algorithm (or FM indexes), using a modular and efficient hardware impl...

[1]  Richard Durbin,et al.  Sequence analysis Fast and accurate short read alignment with Burrows – Wheeler transform , 2009 .

[2]  B. Thyagarajan,et al.  Review of Clinical Next-Generation Sequencing. , 2017, Archives of pathology & laboratory medicine.

[3]  Rosamaria Pinto,et al.  Next-generation sequencing: advances and applications in cancer diagnosis , 2016, OncoTargets and therapy.

[4]  Nuno A. Fonseca,et al.  Tools for mapping high-throughput sequencing data , 2012, Bioinform..

[5]  J. McPherson,et al.  Coming of age: ten years of next-generation sequencing technologies , 2016, Nature Reviews Genetics.

[6]  Cole Trapnell,et al.  Ultrafast and memory-efficient alignment of short DNA sequences to the human genome , 2009, Genome Biology.

[7]  S. Ghorbian,et al.  Clinical Applications of Next-Generation Sequencing in Cancer Diagnosis , 2017, Pathology & Oncology Research.

[8]  Wen-Lian Hsu,et al.  Kart: a divide-and-conquer algorithm for NGS read alignment , 2017, Bioinform..

[9]  Matthew Ruffalo,et al.  Comparative analysis of algorithms for next-generation sequencing read alignment , 2011, Bioinform..

[10]  I. Nookaew,et al.  Evaluation and assessment of read-mapping by multiple next-generation sequencing aligners based on genome-wide characteristics. , 2017, Genomics.

[11]  Wing Hung Wong,et al.  SeqMap: mapping massive amount of oligonucleotides to the genome , 2008, Bioinform..

[12]  Siu-Ming Yiu,et al.  SOAP2: an improved ultrafast tool for short read alignment , 2009, Bioinform..

[13]  Yongchao Liu,et al.  CUSHAW: a CUDA compatible short read aligner to large genomes based on the Burrows-Wheeler transform , 2012, Bioinform..

[14]  Siu-Ming Yiu,et al.  SOAP3: ultra-fast GPU-based parallel alignment tool for short reads , 2012, Bioinform..

[15]  Dominique Lavenier,et al.  GASSST: global alignment short sequence search tool , 2010, Bioinform..