Read simulation software tools | RNA sequencing data analysis
RNA sequencing analysis methods are often derived by relying on hypothetical parametric models for read counts that are not likely to be precisely satisfied in practice. Methods are often tested by analyzing data that have been simulated according to the assumed model.
A data simulation engine and a set of comparative metrics for measuring the accuracy of an inferred alignment. BEERS uses information from a filtered set of the annotated genes, from 11 different annotation efforts, to generate simulated sequence read pairs with characteristics similar to those observed in Illumina sequence reads.
Simulates RNA-seq data, beginning with an experimental design and ending with collections of RNA-seq reads. Its main advantage is the ability to simulate reads indicating isoform-level differential expression across biological replicates for a variety of experimental designs. Data generated by Polyester is a reasonable approximation to real RNA-seq data and standard differential expression workflows can recover differential expression set in the simulation by the user.
Builds a RNA-seq dataset with two independent treatment groups. SimSeq implements a nonparametric simulation algorithm that generates a matrix of RNA-seq read counts by subsampling columns from a large source RNA-seq dataset. Then, the package swaps individual read counts in genes adjusted by a correction factor to create differential expression. It makes no parametric distributional assumptions and preserves the complex gene dependence structure of the original dataset.
A software tool to simulate transcript sets, expression values and sequence reads under a wider range of parameter values and to compare sensitivity, precision and signal-to-noise ratios of different methods. RSSS can be expanded by interested parties to include other methods.
Simulates fusion transcripts. The simulation of events known to create fusion genes and their resulting chimeric proteins is supported, including inter-chromosome translocation, trans-splicing, complex chromosomal rearrangements, and transcriptional read through events. FUSIM provides the ability to assemble a dataset of fusion transcripts useful for testing and benchmarking applications in fusion gene discovery, and enables comprehensive testing in silico of fusion discovery methods in transcriptome sequencing data.
Provides simulated RNA-Seq data that can emulate specific biological mechanism. SimCT is a configurable generator that simulates RNA-Seq data from a reference genome and known transcript annotations. The software supplies data sets which cover cases such as fusion genes. It includes the alignment position and errors of the simulated reads in their names. SimCT is a component of SimBA, a software suite designed to evaluate the performance of an entire RNA-Seq pipeline in the context of a specific biological question.
Simulates whole genome sequencing (WGS) modeled on Chromium Linked Read technology. LRSim allows fine tuning of both the type and number of variants and Illumina read specifications, and full control of important parameters for linked-reads identified in real datasets, including (i) the number of read pairs, (ii) the number of partitions, (iii) the mean molecule length and (iv) the mean number of molecules per partition.
Allows users to produce biologically informative, hierarchical labels with digitally encoded 2D barcodes that can be printed and scanned using another commercial hardware. baRcodeR is a program that can be used for generating unique ID codes, and printable PDF files can be initiated by standard commands. Furthermore, both single-level and hierarchical labels can be created in the command line, interactively or non-interactively.
Simulates specific Illumina RNA-seq datasets properties. rlsim is a package intending to assist users in highlighting individual biasing factors and their interactions on downstream applications. The program is able to replicate protocols dealing with RNA-seq library building including hexamer priming, polymerase chain reaction (PCR) amplification and size selection. Additionally, it also provides a set of features for performing various estimates, such as the assessment of corrected and uncorrected relative expression levels
Generates simulated single-end or paired-end RNA-Seq reads. RNASeqReadSimulator is a set of scripts that provides users an application to allow experienced users to expand functions. It allows users to randomly assign expression levels of transcripts and generate simulated single-end or paired-end RNA-Seq reads. It is also able to simulate random read errors from sequencing platforms. All scripts are command line driven and allows users to invoke and design more functions.
Simulates over dispersed, multiple replica, differential, non-stranded RNA-Seq datasets. RNA Seq Simulator takes SAM alignment files from RNA-Seq data. This method can generate in silico reads. It requires real RNA-seq data as input, and then simulates various types of factors that cause differential gene expression. This tool is part of USeq, a collection of software tools for both low and high level analysis of next generation sequencing (NGS), ultra high throughput signature sequencing data from the Solexa, SOLiD, and 454 platforms.