<> "The repository administrator has not yet configured an RDF license."^^ . <> . . . "NGS-QCbox and Raspberry for Parallel, Automated and Rapid Quality Control Analysis of Large-Scale Next Generation\r\nSequencing (Illumina) Data"^^ . "Rapid popularity and adaptation of next generation sequencing (NGS) approaches have\r\ngenerated huge volumes of data. High throughput platforms like Illumina HiSeq produce\r\nterabytes of raw data that requires quick processing. Quality control of the data is an\r\nimportant component prior to the downstream analyses. To address these issues, we have\r\ndeveloped a quality control pipeline, NGS-QCbox that scales up to process hundreds or\r\nthousands of samples. Raspberry is an in-house tool, developed in C language utilizing\r\nHTSlib (v1.2.1) (http://htslib.org), for computing read/base level statistics. It can be used as\r\nstand-alone application and can process both compressed and uncompressed FASTQ format\r\nfiles. NGS-QCbox integrates Raspberry with other open-source tools for alignment\r\n(Bowtie2), SNP calling (SAMtools) and other utilities (bedtools) towards analyzing raw NGS\r\ndata at higher efficiency and in high-throughput manner. The pipeline implements batch processing\r\nof jobs using Bpipe (https://github.com/ssadedin/bpipe) in parallel and internally, a\r\nfine grained task parallelization utilizing OpenMP. It reports read and base statistics along\r\nwith genome coverage and variants in a user friendly format. The pipeline developed presents\r\na simple menu driven interface and can be used in either quick or complete mode. In\r\naddition, the pipeline in quick mode outperforms in speed against other similar existing QC\r\npipeline/tools. The NGS-QCbox pipeline, Raspberry tool and associated scripts are made\r\navailable at the URL https://github.com/CEG-ICRISAT/NGS-QCbox and https://github.com/\r\nCEG-ICRISAT/Raspberry for rapid quality control analysis of large-scale next generation\r\nsequencing (Illumina) data."^^ . "2015-10" . . "10" . "10" . . "Public Library of Science"^^ . . . "PLOS One"^^ . . . "19326203" . . . . . . . . . . . . . . . . . . . "M"^^ . "Thudi"^^ . "M Thudi"^^ . . "A W"^^ . "Khan"^^ . "A W Khan"^^ . . "D"^^ . "Doddamani"^^ . "D Doddamani"^^ . . "R K"^^ . "Varshney"^^ . "R K Varshney"^^ . . "M A V S K"^^ . "Katta"^^ . "M A V S K Katta"^^ . . . . . . "NGS-QCbox and Raspberry for Parallel, Automated and Rapid Quality Control Analysis of Large-Scale Next Generation\r\nSequencing (Illumina) Data (PDF)"^^ . . . . . "PLOS-2015.pdf"^^ . . . "NGS-QCbox and Raspberry for Parallel, Automated and Rapid Quality Control Analysis of Large-Scale Next Generation\r\nSequencing (Illumina) Data (Other)"^^ . . . . . . "lightbox.jpg"^^ . . . "NGS-QCbox and Raspberry for Parallel, Automated and Rapid Quality Control Analysis of Large-Scale Next Generation\r\nSequencing (Illumina) Data (Other)"^^ . . . . . . "preview.jpg"^^ . . . "NGS-QCbox and Raspberry for Parallel, Automated and Rapid Quality Control Analysis of Large-Scale Next Generation\r\nSequencing (Illumina) Data (Other)"^^ . . . . . . "medium.jpg"^^ . . . "NGS-QCbox and Raspberry for Parallel, Automated and Rapid Quality Control Analysis of Large-Scale Next Generation\r\nSequencing (Illumina) Data (Other)"^^ . . . . . . "small.jpg"^^ . . . "NGS-QCbox and Raspberry for Parallel, Automated and Rapid Quality Control Analysis of Large-Scale Next Generation\r\nSequencing (Illumina) Data (Other)"^^ . . . . . . "indexcodes.txt"^^ . . "HTML Summary of #9623 \n\nNGS-QCbox and Raspberry for Parallel, Automated and Rapid Quality Control Analysis of Large-Scale Next Generation \nSequencing (Illumina) Data\n\n" . "text/html" . . . "Agriculture-Farming, Production, Technology, Economics"@en . .