PRESTO: A toolkit for processing high-throughput sequencing raw reads of lymphocyte receptor repertoires

Jason A. Vander Heiden, Gur Yaari, Mohamed Uduman, Joel N.H. Stern, Kevin C. O'connor, David A. Hafler, Francois Vigneault, Steven H. Kleinstein

Research output: Contribution to journalArticlepeer-review

298 Scopus citations

Abstract

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.

Original languageEnglish
Pages (from-to)1930-1932
Number of pages3
JournalBioinformatics
Volume30
Issue number13
DOIs
StatePublished - 1 Jul 2014

Funding

FundersFunder number
National Institutes of HealthU19AI089992, U19AI050864
National Institute of Allergy and Infectious DiseasesT32AI089704

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