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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…
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rsem-simulate-r…
Desktop

rsem-simulate-reads

Program to simulate RNA-Seq data based on parameters learned from real data…

Program to simulate RNA-Seq data based on parameters learned from real data sets. Part of the RSEM tool.

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BEERS
Desktop

BEERS Benchmarker for Evaluating the Effectiveness of RNA-Seq Software

A data simulation engine and a set of comparative metrics for measuring the…

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…

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SimSeq
Desktop

SimSeq

A data-based simulation algorithm for RNA-seq data. The vector of read counts…

A data-based simulation algorithm for RNA-seq data. The vector of read counts simulated for a given experimental unit has a joint distribution that closely matches the distribution of a source…

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Polyester
Desktop

Polyester

Simulates RNA-seq data, beginning with an experimental design and ending with…

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…

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Spanki
Desktop

Spanki Splicing analysis kit

A set of tools to facilitate analysis of alternative splicing from RNA-SEQ data.

A set of tools to facilitate analysis of alternative splicing from RNA-SEQ data.

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FUSIM
Desktop

FUSIM FUsion SIMulator

Simulates fusion transcripts. The simulation of events known to create fusion…

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,…

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RSSS
Desktop

RSSS

A software tool to simulate transcript sets, expression values and sequence…

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…

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LRSim
Desktop

LRSim Simulator for Linked Reads

Simulates whole genome sequencing (WGS) modeled on Chromium Linked Read…

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…

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compcodeR
Desktop

compcodeR

An R package for benchmarking of differential expression analysis methods, in…

An R package for benchmarking of differential expression analysis methods, in particular methods developed for analyzing RNA-seq data.

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RSS
Desktop

RSS RNA Seq Simulator

Simulates over dispersed, multiple replica, differential, non-stranded RNA-Seq…

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…

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rlsim
Desktop

rlsim

A package for simulating RNA-seq library preparation with parameter estimation.

A package for simulating RNA-seq library preparation with parameter estimation.

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RNASeqReadSimul…
Desktop

RNASeqReadSimulator

Simulates single-end or paired-end RNA-Seq reads. RNASeqReadSimulator is a…

Simulates single-end or paired-end RNA-Seq reads. RNASeqReadSimulator is a Python software that is able to reproduce reads with a user-defined positional bias profile. Additionally, it can be used…

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