P3BSseq: parallel processing pipeline software for automatic analysis of bisulfite sequencing data.
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.



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.



P3BSseq binaries and documentation are available at: http://sourceforge.net/p/p3bsseq/wiki/Home/



mararabra@yahoo.co.uk



Supplementary data are available at Bioinformatics online.
Computational Biology and Bioinformatics, Max Planck Institute for Molecular Biomedicine, Münster, Germany.
Phuc-Loi
PL
Luu
Computational Biology and Systems Biomedicine, Biodonostia Health Research Institute, San Sebastián, Spain.
Daniela
D
Gerovska
Computational Biology and Systems Biomedicine, Biodonostia Health Research Institute, San Sebastián, Spain.
Mikel
M
Arrospide-Elgarresta
Computational Biology and Systems Biomedicine, Biodonostia Health Research Institute, San Sebastián, Spain.
Sugoi
S
Retegi-Carrión
Department of Cell and Developmental Biology, Max Planck Institute for Molecular Biomedicine, Münster, Germany.|Medical Faculty, University of Münster, Münster, Germany.
Hans R
HR
Schöler
Computational Biology and Bioinformatics, Max Planck Institute for Molecular Biomedicine, Münster, Germany.|Computational Biology and Systems Biomedicine, Biodonostia Health Research Institute, San Sebastián, Spain.|IKERBASQUE, Basque Foundation for Science, Bilbao, Spain.
Marcos J
MJ
Araúzo-Bravo
D019175:DNA Methylation; D001330:Electronic Data Processing / Q000379:methods; D023281:Genomics / Q000379:methods; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software; D013447:Sulfites
D013447:Sulfites; C042345:hydrogen sulfite