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LongISLND: in silico sequencing of lengthy and noisy datatypes
Bayo Lau1, Marghoob Mohiyuddin1, John C Mu1
1Roche Sequencing Solutions, Belmont, CA 94002, USA.
Bioinformatics (Oxford, England)
|September 27, 2016
Summary
LongISLND simulates third-generation sequencing data, including Pacific Biosciences (PacBio) multi-pass sequencing. This software aids downstream analysis like variant calling.
Area of Science:
- Bioinformatics
- Computational Biology
- Genomics
Background:
- Third-generation sequencing technologies offer long reads but require specialized data simulation tools.
- Accurate simulation is crucial for developing and validating bioinformatics pipelines.
Purpose of the Study:
- To introduce LongISLND, a novel software package for simulating single-molecule sequencing data.
- To demonstrate the extensibility of LongISLND by emulating Pacific Biosciences (PacBio) sequencing data.
Main Methods:
- LongISLND is implemented in Java.
- The software simulates sequencing data based on third-generation, single-molecule sequencing characteristics.
- Emulation of PacBio P5 and P6 chemistries was performed, generating data in FASTQ, H5, and PacBio BAM formats.
Main Results:
- LongISLND successfully simulates PacBio multi-pass sequencing data.
- The generated data is compatible with standard bioinformatics formats.
- Downstream processing, including consensus building and variant calling, was demonstrated using simulated data.
Conclusions:
- LongISLND provides a valuable tool for simulating long-read sequencing data.
- The software's architecture supports extension to other sequencing technologies.
- It facilitates the development and testing of bioinformatics tools for third-generation sequencing analysis.
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