The DOI matches its Crossref record; 12 of the 12 references it cites were found in a registry or an index.
pRESTO: a toolkit for processing high-throughput sequencing raw reads of lymphocyte receptor repertoires
Open accessAbstract
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. 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 . Contact: steven.kleinstein@yale.edu Supplementary information: Supplementary data are available at Bioinformatics online.
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IgBLAST: an immunoglobulin variable domain sequence analysis tool
Ye, J., Ma, N., Madden, T. L., & Ostell, J. M. (2013) · Nucleic Acids Research · doi:10.1093/nar/gkt382 · Cited by 1,189
Shiroguchi, K., Jia, T. Z., Sims, P. A., & Xie, X. S. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1118018109 · Cited by 276
Rep‐Seq: uncovering the immunological repertoire through next‐generation sequencing
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Yaari, G., Vander Heiden, J. A., Uduman, M., Gadala-Maria, D., Gupta, N., Stern, J. N. H., O’Connor, K. C., Hafler, D. A., Laserson, U., Vigneault, F., et al. (2013) · Frontiers in Immunology · doi:10.3389/fimmu.2013.00358 · Cited by 225
Self-citationGenetic measurement of memory B-cell recall using antibody repertoire sequencing
Vollmers, C., Sit, R. V., Weinstein, J. A., Dekker, C. L., & Quake, S. R. (2013) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1312146110 · Cited by 221
Quantifying selection in high-throughput Immunoglobulin sequencing data sets
Yaari, G., Uduman, M., & Kleinstein, S. H. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks457 · Cited by 192
Self-citationGaëta, B. A., Malming, H. R., Jackson, K., Bain, M., Wilson, P. C., & Collins, A. M. (2007) · Bioinformatics · doi:10.1093/bioinformatics/btm147 · Cited by 128
SoDA: implementation of a 3D alignment algorithm for inference of antigen receptor recombinations
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IgTree©: Creating Immunoglobulin variable region gene lineage trees
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Alameh, M.-G., Tombácz, I., Bettini, E., Lederer, K., Ndeupen, S., Sittplangkoon, C., Wilmore, J. R., Gaudette, B. T., Soliman, O. Y., Pine, M., et al. (2021) · Immunity · doi:10.1016/j.immuni.2021.11.001 · Cited by 775
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Metadata
- Authors
- Vander Heiden, J. A., Yaari, G., Uduman, M., Stern, J. N. H., O’Connor, K. C., Hafler, D. A., Vigneault, F., & Kleinstein, S. H.
- Venue
- Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2014-03-10
- Volume
- 30
- Issue
- 13
- Pages
- 1930-1932
- ISSN
- 1367-4803 (ISSN-L)
- 1367-4811
- OpenAlex
- W2151558930
- Cited by
- 465
- References
- 12
- FWCI
- 6.69
- Type
- journal article
- Language
- en
- Open access
- bronze
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- Vander Heiden, J. A., Yaari, G., Uduman, M., Stern, J. N. H., O’Connor, K. C., Hafler, D. A., Vigneault, F., & Kleinstein, S. H. (2014). pRESTO: a toolkit for processing high-throughput sequencing raw reads of lymphocyte receptor repertoires. Bioinformatics. https://doi.org/10.1093/bioinformatics/btu138
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