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pIRS: Profile-based Illumina pair-end reads simulator.
Xuesong Hu1, Jianying Yuan, Yujian Shi
1BGI-Shenzhen, Shenzhen Biodynamic Optical Imaging Center, Peking University, Beijing, China.
Bioinformatics (Oxford, England)
|April 18, 2012
Summary
A new software, pIRS (profile-based Illumina pair-end reads simulator), accurately simulates Illumina sequencing reads, including error profiles and coverage bias. This tool aids in developing sequencing analysis software and designing future projects.
Area of Science:
- Genomics
- Bioinformatics
Background:
- High-throughput sequencing, particularly Illumina, is crucial for re-sequencing and de novo assembly.
- Existing simulators lack accurate simulation of Illumina read error, quality distributions, and coverage bias.
Purpose of the Study:
- To develop a software package for simulating Illumina sequencing reads with realistic error and quality profiles.
- To address the need for accurate simulation in sequencing data analysis software development and project design.
Main Methods:
- Developed pIRS (profile-based Illumina pair-end reads simulator) using C++ and Perl.
- Trained empirical Base-Calling and GC%-depth profiles from real re-sequencing data.
- Integrated a tool for simulating heterozygous diploid genomes.
Main Results:
- pIRS simulates Illumina reads with error and quality distributions mirroring real sequencing data.
- Simulated coverage bias patterns in pIRS align better with actual data compared to existing simulators.
- The software provides a more realistic simulation environment for sequencing data.
Conclusions:
- pIRS offers a significant improvement over existing simulators for generating realistic Illumina sequencing data.
- The tool is valuable for validating bioinformatics pipelines and optimizing sequencing project strategies.
- pIRS is freely available for academic and research use.
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