Nonlinear Fm Index Application for Alignment of Short Dna Sequences Using Re-Parametrization of Algorithms

Abstract

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 implementation to accelerate alignment programs of short DNA sequence reads. Although these programs use multi-core execution strategies or multiple computers, they have become slow considering the very high speed at which the new massively parallel sequencing machines produce the reads to be aligned. Consequently, a search for different ways to accelerate the alignment is crucial. The proposed design runs with software functions in a hybrid system, and has the ability to align millions of reads to reference as large as the human genome. Tests on the M505k325t card show that a single alignment core can accelerate the computation by a factor close to [Formula: see text] in relation to BWA. Due to the minor consumption of area and power, multiple alignment cores can fill the Field Programmable Gate Array (FPGA) by multiplying the computation speed. With a multiple-core implementation, the processing speed of the design outperforms applications that are accelerated by GPUs and competes with similar FPGA proposals whose cost is much higher.

Field Programmable Gate Array Applications—A Scientometric Review

“…Finally other FPGAs applications in this list includes Hardware-In-the-Loop (HIL) [34,1115,[1276][1277][1278][1279][1280][1281][1282], GPS (Global Positioning System) [1283][1284][1285][1286][1287][1288][1289][1290][1291][1292][1293][1294][1295][1296][1297][1298], Positron Emission Tomography (PET) , bioinformatics [1325][1326][1327][1328][1329][1330][1331][1332][1333][1334][1335][1336][1337][1338][1339][1340][1341][1342], fuzzy logic [1343][1344][1345][1346][1347]…”

ABPSE: Alineador de ADN Basado en Paralelismo a Nivel de Bit y la Estrategia Siembra y Extiende

“…Estas mejoras en la velocidad son muy significantes, puesto que en un proceso normal de alineación, los billones de lecturas que deben alinearse implican días completos de procesamiento, lo cual con ABPSE podría realizarse en solo unas horas. Factores de alineación superiores solo se han reportado mediante aceleradores Hardware basados en unidades de procesamiento gráfico GPUs [26] , o en FPGAs [27] , aunque estas son excelentes opciones, su elevado costo suele ser una limitante. En esta prueba ABPSE utilizó en promedio solo 7.6 GB de memoria RAM, lo cual permite su ejecución en cualquier computadora convencional.…”