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NGS-QCbox and Raspberry for Parallel, Automated and Rapid Quality Control Analysis of Large-Scale Next Generation Sequencing (Illumina) Data

OAR@ICRISAT

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Relation http://oar.icrisat.org/9623/
http://dx.doi.org/10.1371/journal.pone.0139868
10.1371/journal.pone.0139868
 
Title NGS-QCbox and Raspberry for Parallel, Automated and Rapid Quality Control Analysis of Large-Scale Next Generation
Sequencing (Illumina) Data
 
Creator Katta, M A V S K
Khan, A W
Doddamani, D
Thudi, M
Varshney, R K
 
Subject Agriculture-Farming, Production, Technology, Economics
 
Description Rapid popularity and adaptation of next generation sequencing (NGS) approaches have
generated huge volumes of data. High throughput platforms like Illumina HiSeq produce
terabytes of raw data that requires quick processing. Quality control of the data is an
important component prior to the downstream analyses. To address these issues, we have
developed a quality control pipeline, NGS-QCbox that scales up to process hundreds or
thousands of samples. Raspberry is an in-house tool, developed in C language utilizing
HTSlib (v1.2.1) (http://htslib.org), for computing read/base level statistics. It can be used as
stand-alone application and can process both compressed and uncompressed FASTQ format
files. NGS-QCbox integrates Raspberry with other open-source tools for alignment
(Bowtie2), SNP calling (SAMtools) and other utilities (bedtools) towards analyzing raw NGS
data at higher efficiency and in high-throughput manner. The pipeline implements batch processing
of jobs using Bpipe (https://github.com/ssadedin/bpipe) in parallel and internally, a
fine grained task parallelization utilizing OpenMP. It reports read and base statistics along
with genome coverage and variants in a user friendly format. The pipeline developed presents
a simple menu driven interface and can be used in either quick or complete mode. In
addition, the pipeline in quick mode outperforms in speed against other similar existing QC
pipeline/tools. The NGS-QCbox pipeline, Raspberry tool and associated scripts are made
available at the URL https://github.com/CEG-ICRISAT/NGS-QCbox and https://github.com/
CEG-ICRISAT/Raspberry for rapid quality control analysis of large-scale next generation
sequencing (Illumina) data.
 
Publisher Public Library of Science
 
Date 2015-10
 
Type Article
PeerReviewed
 
Format application/pdf
 
Language en
 
Rights —
 
Identifier http://oar.icrisat.org/9623/1/PLOS-2015.pdf
Katta, M A V S K and Khan, A W and Doddamani, D and Thudi, M and Varshney, R K (2015) NGS-QCbox and Raspberry for Parallel, Automated and Rapid Quality Control Analysis of Large-Scale Next Generation Sequencing (Illumina) Data. PLOS One, 10 (10). pp. 1-9. ISSN 1932-6203