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- Title
SCSIM: Jointly simulating correlated single-cell and bulk next-generation DNA sequencing data.
- Authors
Giguere, Collin; Dubey, Harsh Vardhan; Sarsani, Vishal Kumar; Saddiki, Hachem; He, Shai; Flaherty, Patrick
- Abstract
Background: Recently, it has become possible to collect next-generation DNA sequencing data sets that are composed of multiple samples from multiple biological units where each of these samples may be from a single cell or bulk tissue. Yet, there does not yet exist a tool for simulating DNA sequencing data from such a nested sampling arrangement with single-cell and bulk samples so that developers of analysis methods can assess accuracy and precision. Results: We have developed a tool that simulates DNA sequencing data from hierarchically grouped (correlated) samples where each sample is designated bulk or single-cell. Our tool uses a simple configuration file to define the experimental arrangement and can be integrated into software pipelines for testing of variant callers or other genomic tools. Conclusions: The DNA sequencing data generated by our simulator is representative of real data and integrates seamlessly with standard downstream analysis tools.
- Subjects
NUCLEOTIDE sequence; NUCLEOTIDE sequencing; COMPUTER software testing; INTEGRATED software; NEXT generation networks
- Publication
BMC Bioinformatics, 2020, Vol 21, Issue 1, p1
- ISSN
1471-2105
- Publication type
Article
- DOI
10.1186/s12859-020-03550-1