pRESTO statistics

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Citations per year

Number of citations per year for the bioinformatics software tool pRESTO
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Tool usage distribution map

This map represents all the scientific publications referring to pRESTO per scientific context
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Protocols

pRESTO specifications

Information


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

 (9)
library_books

Novel Method for High Throughput Full Length IGHV D J Sequencing of the Immune Repertoire from Bulk B Cells with Single Cell Resolution

2017
Front Immunol
PMCID: 5603803
PMID: 28959265
DOI: 10.3389/fimmu.2017.01157

[…] Processing of raw reads was performed using a custom workflow built with pRESTO (REpertoire Sequencing TOolkit) (). IGHV sequences obtained were then submitted to IMGT/HighV-QUEST () and analyzed using ChangeO (), and custom R scripts. […]

library_books

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

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

[…] ugh 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 were aligned […]

library_books

Overview of methodologies for T cell receptor repertoire analysis

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

[…] s 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 a fea […]

call_split

Data on haplotype supported immunoglobulin germline gene inference

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

[…] llumina, 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 inc […]

library_books

CNS Aquaporin‐4‐specific B cells connect with multiple B‐cell compartments in neuromyelitis optica spectrum disorder

2017
PMCID: 5454399
PMID: 28589164
DOI: 10.1002/acn3.418

[…] The pRESTO workflow was used for data analysis and adopted to our specific primer design and usage of unique molecular identifiers (UMIs). Illumina sequencing reads in FASTQ format were presorted into the […]

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

[…] 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 and trimm […]


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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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