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pRESTO specifications

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Unique identifier OMICS_03443
Name pRESTO
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

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Publication for pRESTO

pRESTO citations

 (7)
library_books

Human Secretory IgM Emerges from Plasma Cells Clonally Related to Gut Memory B Cells and Targets Highly Diverse Commensals

2017
PMCID: 5519504
PMID: 28709802
DOI: 10.1016/j.immuni.2017.06.013

[…] next generation sequencing (table s3). paired-end raw sequencing reads were processed into donor-specific ig gene sequences and grouped in clonal families using a bioinformatics pipeline based on presto, igblast and change-o (, , ). first, raw reads with a phred score lower than 20 were filtered out, and primers for ch and vh genes were masked. next, corresponding paired-end reads […]

library_books

Overview of methodologies for T cell receptor repertoire analysis

2017
PMCID: 5504616
PMID: 28693542
DOI: 10.1186/s12896-017-0379-9

[…] the tool we chose for our analysis, as its parameters may be optimized for different data types, sources and desired outputs. software specific for analysis of data containing umis are migec [] and presto []. the tools listed above are mainly used for primary analysis, as the recovery of tcr sequences from raw data and successive clustering and annotation. lymanalyzer additionally contains […]

library_books

Data on haplotype supported immunoglobulin germline gene inference

2017
PMCID: 5502703
PMID: 28725665
DOI: 10.1016/j.dib.2017.06.031

[…] inc., san diego, ca, usa) at the national genomics infrastructure (scilifelab, stockholm, sweden) . details of sequence output and availability are outlined in . data was pre-processed using presto and change-o as summarized in fig. 1 in ref. . germline gene inference was performed using tigger and igdiscover . additional bioinformatics analysis was performed as outlined elsewhere […]

library_books

Exploration of immunoglobulin transcriptomes from mice immunized with three finger toxins and phospholipases A2 from the Central American coral snake, Micrurus nigrocinctus

2017
PMCID: 5267563
PMID: 28149694
DOI: 10.7717/peerj.2924

[…] read 1, 6 cycles for the index reads, 300 cycles for read 2 and a 10% phix spike-in to increase sequence diversity., miseq reads were demultiplexed using illumina software, and processed with the presto toolsuite () as following: positions with less than phred quality 5 were masked with ns. isotype-specific primers and molecular barcodes (uids or umis) were identified in the amplicon […]

library_books

Individual heritable differences result in unique cell lymphocyte receptor repertoires of naïve and antigen experienced cells

2016
PMCID: 5191574
PMID: 27005435
DOI: 10.1038/ncomms11112

[…] in positions 100–200 of read 2. the resulting individual barcode groups are each assumed to represent multiple reads from a single mrna molecule., additional processing was performed using the presto toolkit. low-quality reads (average phred quality score q<20) were discarded. reads within a umi group were aligned, and a consensus sequence for each umi group was generated (minimum total […]

library_books

Practical guidelines for B cell receptor repertoire sequencing analysis

2015
PMCID: 4654805
PMID: 26589402
DOI: 10.1186/s13073-015-0243-2

[…] read of a pair, it may be necessary to also discard the other read of the pair (if later steps of the analysis depend on having both ends). several tools for this step include pandaseq [], pear [], presto [], and usearch [] (for a broader list and comparison of features see [])., umis are highly diverse nucleotide tags appended to the mrna, usually at the reverse transcription step []. umis […]


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pRESTO institution(s)
Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA; Bioengineering Program, Faculty of Engineering, Bar-Ilan University, Ramat Gan, Israel; Department of Pathology, Yale School of Medicine, New Haven, CT, USA; Department of Science Education, Hofstra North Shore-LIJ School of Medicine, Hofstra University, Hempstead, NY, USA; Department of Neurology, Yale School of Medicine, New Haven, CT, Human and Translational Immunology Program, Yale School of Medicine, New Haven, CT, USA; AbVitro Inc; Boston, MA, USA

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