pRESTO: a toolkit for processing high-throughput sequencing raw reads of lymphocyte receptor repertoires
By J. V. Heiden, G. Yaari, Mohamed Uduman, Joel N.H. Stern, K. O’Connor, David A. Hafler, Francois Vigneault, S. Kleinstein. Bioinform., 2014
451 citations recorded by the source corpus.
UNLABELLED 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. 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.
Subfields: Immunology, Molecular Biology, Radiology, Nuclear Medicine and Imaging
View Paper: https://www.semanticscholar.org/paper/ca321103129928fcc5522d2a314fdd167bf8805e
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