FAssem: FPGA Based Acceleration of De Novo Genome Assembly

Sharat Chandra Varma B; K. Paul; M. Balakrishnan; D. Lavenier

doi:10.1109/FCCM.2013.25

FAssem: FPGA Based Acceleration of De Novo Genome Assembly

Sharat Chandra Varma B, K. Paul, M. Balakrishnan, D. Lavenier

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

20 Citations (Scopus)

Abstract

Next generation sequencing technologies produce large amounts of data at very low cost. They produce short reads of DNA fragments. These fragments have many overlaps, lots of repeats and may also include sequencing errors. The assembly process involves merging these sequences to form the original sequences. In recent years many software programs have been developed for this purpose. All of them take significant amount of time to execute. Velvet is a commonly used de novo assembly program. We propose a method to reduce the overall time for assembly by using pre-processing of the short read data on FPGAs and processing its output using Velvet. We show significant speed-ups with slight or no compromise on the quality of the assembled output.

Original language	English
Title of host publication	2013 IEEE 21st Annual International Symposium on Field-Programmable Custom Computing Machines
Publisher	IEEE Xplore
Pages	173-176
Number of pages	4
ISBN (Electronic)	9780769549699
ISBN (Print)	9781467360050
DOIs	https://doi.org/10.1109/FCCM.2013.25
Publication status	Published (in print/issue) - 25 Jun 2013

Keywords

bioinformatics
DNA
field programmable gate arrays
FAssem
FPGA-based acceleration
De Novo genome assembly
next generation sequencing technologies
DNA fragments
sequencing errors
software programs
Velvet
short read data preprocessing
assembled output quality
Field programmable gate arrays
Assembly
Bioinformatics
Software
Genomics
Acceleration
Redundancy
FPGA
Next Generation Sequencing Assembly

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10.1109/FCCM.2013.25

Cite this

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title = "FAssem: FPGA Based Acceleration of De Novo Genome Assembly",

abstract = "Next generation sequencing technologies produce large amounts of data at very low cost. They produce short reads of DNA fragments. These fragments have many overlaps, lots of repeats and may also include sequencing errors. The assembly process involves merging these sequences to form the original sequences. In recent years many software programs have been developed for this purpose. All of them take significant amount of time to execute. Velvet is a commonly used de novo assembly program. We propose a method to reduce the overall time for assembly by using pre-processing of the short read data on FPGAs and processing its output using Velvet. We show significant speed-ups with slight or no compromise on the quality of the assembled output.",

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author = "B, {Sharat Chandra Varma} and K. Paul and M. Balakrishnan and D. Lavenier",

year = "2013",

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doi = "10.1109/FCCM.2013.25",

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AU - B, Sharat Chandra Varma

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AU - Balakrishnan, M.

AU - Lavenier, D.

PY - 2013/6/25

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N2 - Next generation sequencing technologies produce large amounts of data at very low cost. They produce short reads of DNA fragments. These fragments have many overlaps, lots of repeats and may also include sequencing errors. The assembly process involves merging these sequences to form the original sequences. In recent years many software programs have been developed for this purpose. All of them take significant amount of time to execute. Velvet is a commonly used de novo assembly program. We propose a method to reduce the overall time for assembly by using pre-processing of the short read data on FPGAs and processing its output using Velvet. We show significant speed-ups with slight or no compromise on the quality of the assembled output.

AB - Next generation sequencing technologies produce large amounts of data at very low cost. They produce short reads of DNA fragments. These fragments have many overlaps, lots of repeats and may also include sequencing errors. The assembly process involves merging these sequences to form the original sequences. In recent years many software programs have been developed for this purpose. All of them take significant amount of time to execute. Velvet is a commonly used de novo assembly program. We propose a method to reduce the overall time for assembly by using pre-processing of the short read data on FPGAs and processing its output using Velvet. We show significant speed-ups with slight or no compromise on the quality of the assembled output.

KW - bioinformatics

KW - DNA

KW - field programmable gate arrays

KW - FAssem

KW - FPGA-based acceleration

KW - De Novo genome assembly

KW - next generation sequencing technologies

KW - DNA fragments

KW - sequencing errors

KW - software programs

KW - Velvet

KW - short read data preprocessing

KW - assembled output quality

KW - Field programmable gate arrays

KW - Assembly

KW - Bioinformatics

KW - Software

KW - Genomics

KW - Acceleration

KW - Redundancy

KW - FPGA

KW - Next Generation Sequencing Assembly

U2 - 10.1109/FCCM.2013.25

DO - 10.1109/FCCM.2013.25

M3 - Conference contribution

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SP - 173

EP - 176

BT - 2013 IEEE 21st Annual International Symposium on Field-Programmable Custom Computing Machines

PB - IEEE Xplore

ER -

FAssem: FPGA Based Acceleration of De Novo Genome Assembly

Abstract

Keywords

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