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An Ultrahigh-throughput Microfluidic Platform for Single-cell Genome Sequencing

An Ultrahigh-throughput Microfluidic Platform for Single-cell Genome Sequencing

Published on: May 23, 2018

SCSsim: an integrated tool for simulating single-cell genome sequencing data.

Zhenhua Yu¹, Fang Du¹, Xuehong Sun¹

¹Department of Software Engineering, Ningxia University, Yinchuan 750021, China.

Bioinformatics (Oxford, England)

|October 5, 2019

Summary

This summary is machine-generated.

A new software, SCSsim, simulates single-cell sequencing (SCS) data by mimicking whole-genome amplification. This tool effectively addresses allele dropout and unbalanced amplification for reliable bioinformatics tool benchmarking.

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Area of Science:

Genomics
Bioinformatics
Computational Biology

Background:

Single-cell sequencing (SCS) presents technical challenges like allele dropout (ADO) and unbalanced allele amplification.
Accurate simulation of these issues is crucial for benchmarking SCS bioinformatics tools.
Existing simulators lack whole-genome amplification simulation, limiting their utility for SCS data.

Purpose of the Study:

To develop a novel software package, SCSsim, for efficient and parallel simulation of SCS datasets.
To emulate technical issues inherent in SCS, including whole-genome amplification.

Main Methods:

SCSsim constructs a single-cell genome, incorporating user-defined genomic variations.
It simulates whole-genome amplification using the MALBAC technique.
Sequencing reads are generated based on inferred profiles from amplified products.

Main Results:

SCSsim efficiently simulates SCS datasets with minimal user input.
The software accurately mimics varying ADO rates.
Evaluations confirm its utility for variation detection efficiency and genome coverage simulation.

Conclusions:

SCSsim is a highly efficient and valuable tool for generating realistic single-cell sequencing data.
It provides a robust platform for benchmarking SCS-based bioinformatics tools.
The software addresses limitations of current simulators by incorporating whole-genome amplification.