== Abstract ==

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Prep is a high-performance tool for preparing sequence alignment/map files for variant calling in sequencing pipelines. It can be used as a replacement for SAMtools and Picard for preparation steps such as filtering, sorting, marking duplicates, reordering contigs, and so on, while producing identical results. What sets elPrep apart is its software architecture that allows executing preparation pipelines by making only a single pass through the data, no matter how many preparation steps are used in the pipeline. elPrep is designed as a multithreaded application that runs entirely in memory, avoids repeated file I/O, and merges the computation of several preparation steps to significantly speed up the execution time. For example, for a preparation pipeline of five steps on a whole-exome BAM file (NA12878), we reduce the execution time from about 1: 40 hours, when using a combination of SAMtools and Picard, to about 15 minutes when using elPrep, while utilising the same server resources, here 48 threads and 23GB of RAM. For the same pipeline on whole-genome data (NA12878), elPrep reduces the runtime from 24 hours to less than 5 hours. As a typical clinical study may contain sequencing data for hundreds of patients, elPrep can remove several hundreds of hours of computing time, and thus substantially reduce analysis time and cost.

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Document type: Article

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== Full document ==

<pdf>Media:Draft_Content_712751452-beopen274-1876-document.pdf</pdf>

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== Original document ==

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The different versions of the original document can be found in:

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* [http://europepmc.org/articles/PMC4504710 http://europepmc.org/articles/PMC4504710]

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* [https://dx.doi.org/10.1371/journal.pone.0132868 https://dx.doi.org/10.1371/journal.pone.0132868]

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* [https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0132868&type=printable https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0132868&type=printable] under the license cc-by

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* [http://dx.plos.org/10.1371/journal.pone.0132868 http://dx.plos.org/10.1371/journal.pone.0132868],

: [http://dx.doi.org/10.1371/journal.pone.0132868 http://dx.doi.org/10.1371/journal.pone.0132868] under the license http://creativecommons.org/licenses/by/4.0/

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* [http://europepmc.org/articles/PMC4504710?pdf=render http://europepmc.org/articles/PMC4504710?pdf=render],

: [https://doaj.org/toc/1932-6203 https://doaj.org/toc/1932-6203]

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* [https://biblio.ugent.be/publication/6990489 https://biblio.ugent.be/publication/6990489],

: [http://hdl.handle.net/1854/LU-6990489 http://hdl.handle.net/1854/LU-6990489],

: [http://dx.doi.org/10.1371/journal.pone.0132868 http://dx.doi.org/10.1371/journal.pone.0132868],

: [https://biblio.ugent.be/publication/6990489/file/6990613 https://biblio.ugent.be/publication/6990489/file/6990613]

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* [https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0132868 https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0132868],

: [https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4504710 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4504710],

: [https://biblio.ugent.be/publication/6990489/file/6990613.pdf https://biblio.ugent.be/publication/6990489/file/6990613.pdf],

: [http://europepmc.org/articles/PMC4504710 http://europepmc.org/articles/PMC4504710],

: [https://core.ac.uk/display/55710472 https://core.ac.uk/display/55710472],

: [http://ui.adsabs.harvard.edu/abs/2015PLoSO..1032868H/abstract http://ui.adsabs.harvard.edu/abs/2015PLoSO..1032868H/abstract],

: [https://biblio.ugent.be/publication/6990489 https://biblio.ugent.be/publication/6990489],

: [https://dx.plos.org/10.1371/journal.pone.0132868 https://dx.plos.org/10.1371/journal.pone.0132868],

: [https://paperity.org/p/73482480/elprep-high-performance-preparation-of-sequence-alignment-map-files-for-variant-calling https://paperity.org/p/73482480/elprep-high-performance-preparation-of-sequence-alignment-map-files-for-variant-calling],

: [https://academic.microsoft.com/#/detail/859230734 https://academic.microsoft.com/#/detail/859230734]

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