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          Institute: MPI für molekulare Biomedizin     Collection: Jahrbuch 2018 (publ. 2017, arch)     Display Documents



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ID: 744127.0, MPI für molekulare Biomedizin / Jahrbuch 2018 (publ. 2017, arch)
P3BSseq: parallel processing pipeline software for automatic analysis of bisulfite sequencing data
Authors:Luu, P. L.; Gerovska, D.; Arrospide-Elgarresta, M.; Retegi-Carrion, S.; Scholer, H. R.; Arauzo-Bravo, M. J.
Date of Publication (YYYY-MM-DD):2017-02-01
Title of Journal:Bioinformatics
Volume:33
Issue / Number:3
Start Page:428
End Page:431
Review Status:Internal review
Audience:Not Specified
Abstract / Description:Motivation: Bisulfite sequencing (BSseq) processing is among the most cumbersome next generation sequencing (NGS) applications. Though some BSseq processing tools are available, they are scattered, require puzzling parameters and are running-time and memory-usage demanding. Results: We developed P3BSseq, a parallel processing pipeline for fast, accurate and automatic analysis of BSseq reads that trims, aligns, annotates, records the intermediate results, performs bisulfite conversion quality assessment, generates BED methylome and report files following the NIH standards. P3BSseq outperforms the known BSseq mappers regarding running time, computer hardware requirements (processing power and memory use) and is optimized to process the upcoming, extended BSseq reads. We optimized the P3BSseq parameters for directional and non-directional libraries, and for single-end and paired-end reads of Whole Genome and Reduced Representation BSseq. P3BSseq is a user-friendly streamlined solution for BSseq upstream analysis, requiring only basic computer and NGS knowledge. Availability and Implementation: P3BSseq binaries and documentation are available at: http://sourceforge.net/p/p3bsseq/wiki/Home/ Contact: mararabra@yahoo.co.uk Supplimentary Information: Supplementary data are available at Bioinformatics online.
Free Keywords:Automatic Data Processing/methods; *DNA Methylation; Genomics/methods; High-Throughput Nucleotide Sequencing/*methods; Humans; Sequence Analysis, DNA/*methods; *Software; Sulfites
External Publication Status:published
Document Type:Article
Communicated by:MPI für molekulare Biomedizin
Affiliations:MPI für molekulare Biomedizin
External Affiliations:Computational Biology and Systems Biomedicine, Biodonostia Health Research Institute, San Sebastian, Spain. Department of Cell and Developmental Biology, Max Planck Institute for Molecular Biomedicine, Munster, Germany. Medical Faculty, University of Munster, Munster, Germany. IKERBASQUE, Basque Foundation for Science, Bilbao, Spain.
Identifiers:ISSN:1367-4811 (Electronic) 1367-4803 (Linking) %R 10.1... [ID No:1]
URL:https://www.ncbi.nlm.nih.gov/pubmed/28172520 [ID No:2]
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