NGS-QCbox and Raspberry for Parallel, Automated and Rapid Quality Control Analysis of Large-Scale Next Generation Sequencing (Illumina) Data
Identifieur interne : 000088 ( Main/Merge ); précédent : 000087; suivant : 000089NGS-QCbox and Raspberry for Parallel, Automated and Rapid Quality Control Analysis of Large-Scale Next Generation Sequencing (Illumina) Data
Auteurs : Mohan A. V. S. K. Katta [Inde] ; Aamir W. Khan [Inde] ; Dadakhalandar Doddamani [Inde] ; Mahendar Thudi [Inde] ; Rajeev K. Varshney [Inde, Australie]Source :
- PLoS ONE [ 1932-6203 ] ; 2015.
Abstract
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) (
Url:
DOI: 10.1371/journal.pone.0139868
PubMed: 26460497
PubMed Central: 4604202
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V. S. K." last="Katta">Mohan A. V. S. K. Katta</name><affiliation wicri:level="1"><nlm:aff id="aff001"><addr-line>International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India</addr-line></nlm:aff><country xml:lang="fr">Inde</country><wicri:regionArea>International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad</wicri:regionArea><wicri:noRegion>Hyderabad</wicri:noRegion></affiliation></author><author><name sortKey="Khan, Aamir W" sort="Khan, Aamir W" uniqKey="Khan A" first="Aamir W." last="Khan">Aamir W. Khan</name><affiliation wicri:level="1"><nlm:aff id="aff001"><addr-line>International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India</addr-line></nlm:aff><country xml:lang="fr">Inde</country><wicri:regionArea>International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad</wicri:regionArea><wicri:noRegion>Hyderabad</wicri:noRegion></affiliation></author><author><name sortKey="Doddamani, Dadakhalandar" sort="Doddamani, Dadakhalandar" uniqKey="Doddamani D" first="Dadakhalandar" last="Doddamani">Dadakhalandar Doddamani</name><affiliation wicri:level="1"><nlm:aff id="aff001"><addr-line>International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India</addr-line></nlm:aff><country xml:lang="fr">Inde</country><wicri:regionArea>International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad</wicri:regionArea><wicri:noRegion>Hyderabad</wicri:noRegion></affiliation></author><author><name sortKey="Thudi, Mahendar" sort="Thudi, Mahendar" uniqKey="Thudi M" first="Mahendar" last="Thudi">Mahendar Thudi</name><affiliation wicri:level="1"><nlm:aff id="aff001"><addr-line>International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India</addr-line></nlm:aff><country xml:lang="fr">Inde</country><wicri:regionArea>International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad</wicri:regionArea><wicri:noRegion>Hyderabad</wicri:noRegion></affiliation></author><author><name sortKey="Varshney, Rajeev K" sort="Varshney, Rajeev K" uniqKey="Varshney R" first="Rajeev K." last="Varshney">Rajeev K. Varshney</name><affiliation wicri:level="1"><nlm:aff id="aff001"><addr-line>International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India</addr-line></nlm:aff><country xml:lang="fr">Inde</country><wicri:regionArea>International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad</wicri:regionArea><wicri:noRegion>Hyderabad</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:aff id="aff002"><addr-line>School of Plant Biology and Institute of Agriculture, The University of Western Australia, Crawley, Australia</addr-line></nlm:aff><country xml:lang="fr">Australie</country><wicri:regionArea>School of Plant Biology and Institute of Agriculture, The University of Western Australia, Crawley</wicri:regionArea><wicri:noRegion>Crawley</wicri:noRegion></affiliation></author></analytic><series><title level="j">PLoS ONE</title><idno type="eISSN">1932-6203</idno><imprint><date when="2015">2015</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>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) (<ext-link ext-link-type="uri" xlink:href="http://htslib.org/">http://htslib.org</ext-link>), 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 (<ext-link ext-link-type="uri" xlink:href="https://github.com/ssadedin/bpipe">https://github.com/ssadedin/bpipe</ext-link>) 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 <italic>quick</italic> or <italic>complete</italic> mode. In addition, the pipeline in <italic>quick</italic> 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 <ext-link ext-link-type="uri" xlink:href="https://github.com/CEG-ICRISAT/NGS-QCbox">https://github.com/CEG-ICRISAT/NGS-QCbox</ext-link> and <ext-link ext-link-type="uri" xlink:href="https://github.com/CEG-ICRISAT/Raspberry">https://github.com/CEG-ICRISAT/Raspberry</ext-link> for rapid quality control analysis of large-scale next generation sequencing (Illumina) data.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Thudi, M" uniqKey="Thudi M">M Thudi</name></author><author><name sortKey="Li, Y" uniqKey="Li Y">Y Li</name></author><author><name sortKey="Jackson, Sa" uniqKey="Jackson S">SA Jackson</name></author><author><name sortKey="May, Gd" uniqKey="May G">GD May</name></author><author><name sortKey="Varshney, Rk" uniqKey="Varshney R">RK Varshney</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Mccouch, S" 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sortKey="Huang, W" uniqKey="Huang W">W Huang</name></author><author><name sortKey="Li, L" uniqKey="Li L">L Li</name></author><author><name sortKey="Myers, Jr" uniqKey="Myers J">JR Myers</name></author><author><name sortKey="Marth, Gt" uniqKey="Marth G">GT Marth</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Goff, Sa" uniqKey="Goff S">SA Goff</name></author><author><name sortKey="Vaughn, M" uniqKey="Vaughn M">M Vaughn</name></author><author><name sortKey="Mckay, S" uniqKey="Mckay S">S McKay</name></author><author><name sortKey="Lyons, E" uniqKey="Lyons E">E Lyons</name></author><author><name sortKey="Stapleton, Ae" uniqKey="Stapleton A">AE Stapleton</name></author><author><name sortKey="Gessler, D" uniqKey="Gessler D">D Gessler</name></author></analytic></biblStruct></listBibl></div1></back></TEI></record>Pour manipuler ce document sous Unix (Dilib)
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