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        <dc:title>NGS-QCbox and Raspberry for Parallel, Automated and Rapid Quality Control Analysis of Large-Scale Next Generation&#13;
Sequencing (Illumina) Data</dc:title>
        <dc:creator>Katta, M A V S K</dc:creator>
        <dc:creator>Khan, A W</dc:creator>
        <dc:creator>Doddamani, D</dc:creator>
        <dc:creator>Thudi, M</dc:creator>
        <dc:creator>Varshney, R K</dc:creator>
        <dc:subject>Agriculture-Farming, Production, Technology, Economics</dc:subject>
        <dc:description>Rapid popularity and adaptation of next generation sequencing (NGS) approaches have&#13;
generated huge volumes of data. High throughput platforms like Illumina HiSeq produce&#13;
terabytes of raw data that requires quick processing. Quality control of the data is an&#13;
important component prior to the downstream analyses. To address these issues, we have&#13;
developed a quality control pipeline, NGS-QCbox that scales up to process hundreds or&#13;
thousands of samples. Raspberry is an in-house tool, developed in C language utilizing&#13;
HTSlib (v1.2.1) (http://htslib.org), for computing read/base level statistics. It can be used as&#13;
stand-alone application and can process both compressed and uncompressed FASTQ format&#13;
files. NGS-QCbox integrates Raspberry with other open-source tools for alignment&#13;
(Bowtie2), SNP calling (SAMtools) and other utilities (bedtools) towards analyzing raw NGS&#13;
data at higher efficiency and in high-throughput manner. The pipeline implements batch processing&#13;
of jobs using Bpipe (https://github.com/ssadedin/bpipe) in parallel and internally, a&#13;
fine grained task parallelization utilizing OpenMP. It reports read and base statistics along&#13;
with genome coverage and variants in a user friendly format. The pipeline developed presents&#13;
a simple menu driven interface and can be used in either quick or complete mode. In&#13;
addition, the pipeline in quick mode outperforms in speed against other similar existing QC&#13;
pipeline/tools. The NGS-QCbox pipeline, Raspberry tool and associated scripts are made&#13;
available at the URL https://github.com/CEG-ICRISAT/NGS-QCbox and https://github.com/&#13;
CEG-ICRISAT/Raspberry for rapid quality control analysis of large-scale next generation&#13;
sequencing (Illumina) data.</dc:description>
        <dc:publisher>Public Library of Science</dc:publisher>
        <dc:date>2015-10</dc:date>
        <dc:type>Article</dc:type>
        <dc:type>PeerReviewed</dc:type>
        <dc:format>application/pdf</dc:format>
        <dc:language>en</dc:language>
        <dc:identifier>http://oar.icrisat.org/9623/1/PLOS-2015.pdf</dc:identifier>
        <dc:identifier>  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     </dc:identifier>
        <dc:relation>http://dx.doi.org/10.1371/journal.pone.0139868</dc:relation>
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