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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 in publications

 (7)
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 […]

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 […]

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 […]

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 […]

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 […]


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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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