Comprehensive simulation of metagenomic sequencing data with non‐uniform sampling distribution

Quantitative Biology - Tập 6 Số 2 - Trang 175-185 - 2018
Shansong Liu1, Kui Hua1, Sijie Chen1, Xuegong Zhang1
1MOE Key Lab of Bioinformatics, Bioinformatics Division, TNLIST and Department of Automation, Tsinghua University, Beijing 100084, China

Tóm tắt

BackgroundMetagenomic sequencing is a complex sampling procedure from unknown mixtures of many genomes. Having metagenome data with known genome compositions is essential for both benchmarking bioinformatics software and for investigating influences of various factors on the data. Compared to data from real microbiome samples or from defined microbial mock community, simulated data with proper computational models are better for the purpose as they provide more flexibility for controlling multiple factors.MethodsWe developed a non‐uniform metagenomic sequencing simulation system (nuMetaSim) that is capable of mimicking various factors in real metagenomic sequencing to reflect multiple properties of real data with customizable parameter settings.ResultsWe generated 9 comprehensive metagenomic datasets with different composition complexity from of 203 bacterial genomes and 2 archaeal genomes related with human intestine system.ConclusionThe data can serve as benchmarks for comparing performance of different methods at different situations, and the software package allows users to generate simulation data that can better reflect the specific properties in their scenarios.

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Quantitative Biology

Tập 6 Số 2

175-185

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