{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,27]],"date-time":"2026-10-27T07:23:58Z","timestamp":1793085838571,"version":"4.5.0"},"reference-count":13,"publisher":"Oxford University Press (OUP)","issue":"13","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2014,7,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Summary: Driven by dramatic technological improvements, large-scale characterization of lymphocyte receptor repertoires via high-throughput sequencing is now feasible. Although promising, the high germline and somatic diversity, especially of B-cell immunoglobulin repertoires, presents challenges for analysis requiring the development of specialized computational pipelines. We developed the REpertoire Sequencing TOolkit (pRESTO) for processing reads from high-throughput lymphocyte receptor studies. pRESTO processes raw sequences to produce error-corrected, sorted and annotated sequence sets, along with a wealth of metrics at each step. The toolkit supports multiplexed primer pools, single- or paired-end reads and emerging technologies that use single-molecule identifiers. pRESTO has been tested on data generated from Roche and Illumina platforms. It has a built-in capacity to parallelize the work between available processors and is able to efficiently process millions of sequences generated by typical high-throughput projects.<\/jats:p>\n                  <jats:p>Availability and implementation: pRESTO is freely available for academic use. The software package and detailed tutorials may be downloaded from http:\/\/clip.med.yale.edu\/presto .<\/jats:p>\n                  <jats:p>Contact: \u00a0steven.kleinstein@yale.edu<\/jats:p>\n                  <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btu138","type":"journal-article","created":{"date-parts":[[2014,3,11]],"date-time":"2014-03-11T20:16:49Z","timestamp":1394569009000},"page":"1930-1932","source":"Crossref","is-referenced-by-count":518,"title":["pRESTO: a toolkit for processing high-throughput sequencing raw reads of lymphocyte receptor repertoires"],"prefix":"10.1093","volume":"30","author":[{"given":"Jason A.","family":"Vander Heiden","sequence":"first","affiliation":[{"name":"1 Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06511, USA, 2 Bioengineering Program, Faculty of Engineering, Bar-Ilan University, Ramat Gan 52900, Israel, 3 Department of Pathology, Yale School of Medicine, New Haven, CT 06511, 4 Department of Science Education, Hofstra North Shore-LIJ School of Medicine, Hofstra University, Hempstead, NY 11530, 5 Department of Neurology, Yale School of Medicine, New Haven, CT 06511, 6 Human and Translational Immunology Program, Yale School of Medicine, New Haven, CT 06511 and 7 AbVitro Inc., Boston, MA 02210, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gur","family":"Yaari","sequence":"additional","affiliation":[{"name":"1 Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06511, USA, 2 Bioengineering Program, Faculty of Engineering, Bar-Ilan University, Ramat Gan 52900, Israel, 3 Department of Pathology, Yale School of Medicine, New Haven, CT 06511, 4 Department of Science Education, Hofstra North Shore-LIJ School of Medicine, Hofstra University, Hempstead, NY 11530, 5 Department of Neurology, Yale School of Medicine, New Haven, CT 06511, 6 Human and Translational Immunology Program, Yale School of Medicine, New Haven, CT 06511 and 7 AbVitro Inc., Boston, MA 02210, USA"},{"name":"1 Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06511, USA, 2 Bioengineering Program, Faculty of Engineering, Bar-Ilan University, Ramat Gan 52900, Israel, 3 Department of Pathology, Yale School of Medicine, New Haven, CT 06511, 4 Department of Science Education, Hofstra North Shore-LIJ School of Medicine, Hofstra University, Hempstead, NY 11530, 5 Department of Neurology, Yale School of Medicine, New Haven, CT 06511, 6 Human and Translational Immunology Program, Yale School of Medicine, New Haven, CT 06511 and 7 AbVitro Inc., Boston, MA 02210, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mohamed","family":"Uduman","sequence":"additional","affiliation":[{"name":"1 Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06511, USA, 2 Bioengineering Program, Faculty of Engineering, Bar-Ilan University, Ramat Gan 52900, Israel, 3 Department of Pathology, Yale School of Medicine, New Haven, CT 06511, 4 Department of Science Education, Hofstra North Shore-LIJ School of Medicine, Hofstra University, Hempstead, NY 11530, 5 Department of Neurology, Yale School of Medicine, New Haven, CT 06511, 6 Human and Translational Immunology Program, Yale School of Medicine, New Haven, CT 06511 and 7 AbVitro Inc., Boston, MA 02210, USA"},{"name":"1 Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06511, USA, 2 Bioengineering Program, Faculty of Engineering, Bar-Ilan University, Ramat Gan 52900, Israel, 3 Department of Pathology, Yale School of Medicine, New Haven, CT 06511, 4 Department of Science Education, Hofstra North Shore-LIJ School of Medicine, Hofstra University, Hempstead, NY 11530, 5 Department of Neurology, Yale School of Medicine, New Haven, CT 06511, 6 Human and Translational Immunology Program, Yale School of Medicine, New Haven, CT 06511 and 7 AbVitro Inc., Boston, MA 02210, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Joel N.H.","family":"Stern","sequence":"additional","affiliation":[{"name":"1 Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06511, USA, 2 Bioengineering Program, Faculty of Engineering, Bar-Ilan University, Ramat Gan 52900, Israel, 3 Department of Pathology, Yale School of Medicine, New Haven, CT 06511, 4 Department of Science Education, Hofstra North Shore-LIJ School of Medicine, Hofstra University, Hempstead, NY 11530, 5 Department of Neurology, Yale School of Medicine, New Haven, CT 06511, 6 Human and Translational Immunology Program, Yale School of Medicine, New Haven, CT 06511 and 7 AbVitro Inc., Boston, MA 02210, USA"},{"name":"1 Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06511, USA, 2 Bioengineering Program, Faculty of Engineering, Bar-Ilan University, Ramat Gan 52900, Israel, 3 Department of Pathology, Yale School of Medicine, New Haven, CT 06511, 4 Department of Science Education, Hofstra North Shore-LIJ School of Medicine, Hofstra University, Hempstead, NY 11530, 5 Department of Neurology, Yale School of Medicine, New Haven, CT 06511, 6 Human and Translational Immunology Program, Yale School of Medicine, New Haven, CT 06511 and 7 AbVitro Inc., Boston, MA 02210, USA"},{"name":"1 Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06511, USA, 2 Bioengineering Program, Faculty of Engineering, Bar-Ilan University, Ramat Gan 52900, Israel, 3 Department of Pathology, Yale School of Medicine, New Haven, CT 06511, 4 Department of Science Education, Hofstra North Shore-LIJ School of Medicine, Hofstra University, Hempstead, NY 11530, 5 Department of Neurology, Yale School of Medicine, New Haven, CT 06511, 6 Human and Translational Immunology Program, Yale School of Medicine, New Haven, CT 06511 and 7 AbVitro Inc., Boston, MA 02210, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kevin C.","family":"O\u2019Connor","sequence":"additional","affiliation":[{"name":"1 Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06511, USA, 2 Bioengineering Program, Faculty of Engineering, Bar-Ilan University, Ramat Gan 52900, Israel, 3 Department of Pathology, Yale School of Medicine, New Haven, CT 06511, 4 Department of Science Education, Hofstra North Shore-LIJ School of Medicine, Hofstra University, Hempstead, NY 11530, 5 Department of Neurology, Yale School of Medicine, New Haven, CT 06511, 6 Human and Translational Immunology Program, Yale School of Medicine, New Haven, CT 06511 and 7 AbVitro Inc., Boston, MA 02210, USA"},{"name":"1 Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06511, USA, 2 Bioengineering Program, Faculty of Engineering, Bar-Ilan University, Ramat Gan 52900, Israel, 3 Department of Pathology, Yale School of Medicine, New Haven, CT 06511, 4 Department of Science Education, Hofstra North Shore-LIJ School of Medicine, Hofstra University, Hempstead, NY 11530, 5 Department of Neurology, Yale School of Medicine, New Haven, CT 06511, 6 Human and Translational Immunology Program, Yale School of Medicine, New Haven, CT 06511 and 7 AbVitro Inc., Boston, MA 02210, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"David A.","family":"Hafler","sequence":"additional","affiliation":[{"name":"1 Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06511, USA, 2 Bioengineering Program, Faculty of Engineering, Bar-Ilan University, Ramat Gan 52900, Israel, 3 Department of Pathology, Yale School of Medicine, New Haven, CT 06511, 4 Department of Science Education, Hofstra North Shore-LIJ School of Medicine, Hofstra University, Hempstead, NY 11530, 5 Department of Neurology, Yale School of Medicine, New Haven, CT 06511, 6 Human and Translational Immunology Program, Yale School of Medicine, New Haven, CT 06511 and 7 AbVitro Inc., Boston, MA 02210, USA"},{"name":"1 Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06511, USA, 2 Bioengineering Program, Faculty of Engineering, Bar-Ilan University, Ramat Gan 52900, Israel, 3 Department of Pathology, Yale School of Medicine, New Haven, CT 06511, 4 Department of Science Education, Hofstra North Shore-LIJ School of Medicine, Hofstra University, Hempstead, NY 11530, 5 Department of Neurology, Yale School of Medicine, New Haven, CT 06511, 6 Human and Translational Immunology Program, Yale School of Medicine, New Haven, CT 06511 and 7 AbVitro Inc., Boston, MA 02210, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Francois","family":"Vigneault","sequence":"additional","affiliation":[{"name":"1 Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06511, USA, 2 Bioengineering Program, Faculty of Engineering, Bar-Ilan University, Ramat Gan 52900, Israel, 3 Department of Pathology, Yale School of Medicine, New Haven, CT 06511, 4 Department of Science Education, Hofstra North Shore-LIJ School of Medicine, Hofstra University, Hempstead, NY 11530, 5 Department of Neurology, Yale School of Medicine, New Haven, CT 06511, 6 Human and Translational Immunology Program, Yale School of Medicine, New Haven, CT 06511 and 7 AbVitro Inc., Boston, MA 02210, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Steven H.","family":"Kleinstein","sequence":"additional","affiliation":[{"name":"1 Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, New 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