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 have 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. We optimized the P3BSseq parameters for both directional and non-directional libraries, and for both 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.

Features

  • Next Generation Sequencing (NGS) data processing
  • DNA methylomics analysis
  • Parallel processing
  • Reduced Representation of Bisulfite Sequencing (RRBS)

Project Samples

P3BSseq flow diagram of the pipelines for single-end and paired-end reads processing. S1 – S6, and P1 - P8 are the different thresholds regulating the decision process for single-end and for paired-end reads respectively, they have default values and can be tuned in the parameter file. The block gray colors are proportional to the number of parallel processes (darker color corresponds to more processes running in parallel) Five folder structure associated to the use of P3BSseq. The REFERENCE GENOME folder hosts the different reference genomes, their annotation and indexing. Once a reference genome has been downloaded and indexed, further processing is not necessary. INPUT FILES folder hosts the raw reads in fastq format of each methylomics sample to be processed. P3BSseq folder hosts the P3BSseq software. OUTPUT folder hosts the output subfolders and files associated with each methylomics sample processed. The names of the five main folders can be changed by the user. To allow the executable files of P3BSseq to find them, the names of the five main folders have to be provided in the parameter files of the PARAMETER folder. The legend to the right shows the types of folders and files. P3BSseq parallel flow-time diagram. Example of processing of the main steps on three CPUs of a methylome split into five files. The numbers denote input files and their corresponding thread indexes. The horizontal block arrows mark the thread of each task, their length; height and color mark the time occupancy of each core for processing each file, the required memory and the step type, respectively.

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Categories

Bio-Informatics

License

Creative Commons Attribution License

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Additional Project Details

Languages

English

Intended Audience

Science/Research

User Interface

Console/Terminal

Programming Language

Python

Related Categories

Python Bio-Informatics Software

Registered

2015-01-14
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