NDLI: Removing Sequential Bottlenecks in Analysis of Next-Generation Sequencing Data

Content Provider	IEEE Xplore Digital Library
Author	Yi Wang Agrawal, G. Ozer, G. Kun Huang
Copyright Year	2014
Description	Author affiliation: Biomed. Inf., Ohio State Univ., Columbus, OH, USA (Ozer, G.; Kun Huang) \|\| Comput. Sci. & Eng., Ohio State Univ., Columbus, OH, USA (Yi Wang; Agrawal, G.)
Abstract	Throughput from sequencing instruments has been increasing in an unprecedented speed, leading to an explosion of the next-generation sequencing (NGS) data, and challenges in storing, managing, and analyzing these datasets. Parallelism is the key in handling large-scale data, and some progress has been made in parallelizing important steps, like sequence alignment. However, other major steps continue to be sequential, limiting the ability to handle massive datasets. In this paper, we focus on parallelizing algorithms from two areas. The first is efficient data format conversion among a wide variety of sequence data formats, which is important for cross-utilization of different analysis modules. The second is statistical analysis. Our parallelization sequence data format converter allows sequence datasets in BAM/SAM format to be converted into multiple formats, including SAM/BAM, BED, FASTA, FASTQ, BEDGRAPH, JSON, and YAML, using both shared memory and distributed memory parallelism. The converter currently comprises three instances: SAM format converter, BAM format converter and preprocessing-optimized SAM format converter. Additionally, our converter can also support partial format conversion, to perform format conversion only on a specified chromosome region. The statistical analysis module includes parallelized non-local means (NL-means) algorithm and false discovery rate (FDR) computation. Through extensive evaluation, we demonstrate high scalability of our framework.
Starting Page	508
Ending Page	517
File Size	343168
Page Count	10
File Format	PDF
e-ISBN	9781479941162
DOI	10.1109/IPDPSW.2014.64
Language	English
Publisher	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Publisher Date	2014-05-19
Publisher Place	USA
Access Restriction	Subscribed
Rights Holder	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Subject Keyword	Algorithm design and analysis Sequential analysis Histograms Program processors Statistical analysis Genomics Bioinformatics Statistical Analysis Parallelization Next-Generation Sequencing Data Format Conversion
Content Type	Text
Resource Type	Article

Sl.	Authority	Responsibilities	Communication Details
1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
2	Indian Institute of Technology Kharagpur	Host Institute of the Project: The host institute of the project is responsible for providing infrastructure support and hosting the project	https://www.iitkgp.ac.in
3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
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9	IDR Setup or Support	Queries related to establishment and support of Institutional Digital Repository (IDR) and IDR workshops	idr@ndl.gov.in

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