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Brooks TG, Lahens NF, Mrčela A, Sarantopoulou D, Nayak S, Naik A, Sengupta S, Choi PS, Grant GR. BEERS2: RNA-Seq simulation through high fidelity in silico modeling. Brief Bioinform 2024; 25:bbae164. [PMID: 38605641 PMCID: PMC11009461 DOI: 10.1093/bib/bbae164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 01/26/2024] [Accepted: 03/26/2024] [Indexed: 04/13/2024] Open
Abstract
Simulation of RNA-seq reads is critical in the assessment, comparison, benchmarking and development of bioinformatics tools. Yet the field of RNA-seq simulators has progressed little in the last decade. To address this need we have developed BEERS2, which combines a flexible and highly configurable design with detailed simulation of the entire library preparation and sequencing pipeline. BEERS2 takes input transcripts (typically fully length messenger RNA transcripts with polyA tails) from either customizable input or from CAMPAREE simulated RNA samples. It produces realistic reads of these transcripts as FASTQ, SAM or BAM formats with the SAM or BAM formats containing the true alignment to the reference genome. It also produces true transcript-level quantification values. BEERS2 combines a flexible and highly configurable design with detailed simulation of the entire library preparation and sequencing pipeline and is designed to include the effects of polyA selection and RiboZero for ribosomal depletion, hexamer priming sequence biases, GC-content biases in polymerase chain reaction (PCR) amplification, barcode read errors and errors during PCR amplification. These characteristics combine to make BEERS2 the most complete simulation of RNA-seq to date. Finally, we demonstrate the use of BEERS2 by measuring the effect of several settings on the popular Salmon pseudoalignment algorithm.
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Affiliation(s)
- Thomas G Brooks
- Institute for Translational Medicine and Therapeutics, University of Pennsylvania, PA, USA
| | - Nicholas F Lahens
- Institute for Translational Medicine and Therapeutics, University of Pennsylvania, PA, USA
| | - Antonijo Mrčela
- Institute for Translational Medicine and Therapeutics, University of Pennsylvania, PA, USA
| | - Dimitra Sarantopoulou
- Institute for Translational Medicine and Therapeutics, University of Pennsylvania, PA, USA
- Current address: National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Soumyashant Nayak
- Institute for Translational Medicine and Therapeutics, University of Pennsylvania, PA, USA
- Current address: Statistics and Mathematics Unit, Indian Statistical Institute, Bengaluru, Karnataka, India
| | - Amruta Naik
- Institute for Translational Medicine and Therapeutics, University of Pennsylvania, PA, USA
- Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Shaon Sengupta
- Institute for Translational Medicine and Therapeutics, University of Pennsylvania, PA, USA
- Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Peter S Choi
- Division of Cancer Pathobiology, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pathology & Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Gregory R Grant
- Institute for Translational Medicine and Therapeutics, University of Pennsylvania, PA, USA
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
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