Read Simulators
Short Read Simulators
With the popularity of next-generation sequencing (NGS) technologies, many NGS read simulators have been developed. Currently, many of the popular short read simulators are designed to simulate reads mimicking many Illumina, 454 and SOLiD platforms. Listed below are some popular short read simulators. Links to their publications are provided as well.
Long Read Simulators
With the advancements in sequencing technologies, scientists have shown an increasing interest in using third-generation sequencing (TGS) technologies. Currently, many of the popular long read simulators are designed to simulate reads mimicking the two main TGS technologies; (1) Pacific Biosciences (PacBio) and (2) Oxford Nanopore (ONT). Listed below are some of the popular and recently introduced PacBio and ONT simulators. Links to their publications are provided as well.
PacBio Simulators
ONT Simulators
Comments
There are several tools available for short read simulators that are widely used in bioinformatics research. Here are some of them:
ART: The ART (short for Artificial Read Simulator) is a popular tool for generating synthetic reads based on sequencing technologies such as Illumina, SOLiD, and 454. It is a versatile tool that allows users to simulate reads with different error rates, read lengths, and insert sizes. The ART is open-source and available for free download.
wgsim: wgsim is another widely used short read simulator that generates synthetic reads based on the whole genome sequencing technology. It can simulate reads with different read lengths, error rates, and coverage levels. The wgsim tool is also open-source and available for free download.
PIRS: PIRS (short for Profile-based Illumina pair-end Reads Simulator) is a short read simulator that uses a profile-based approach to generate synthetic reads. It can simulate reads with different sequencing technologies, including Illumina, Ion Torrent, and PacBio. PIRS allows users to customize different sequencing parameters, such as error rates, read lengths, and insert sizes.
SimSeq: SimSeq is a Python-based short read simulator that allows users to simulate reads from different sequencing platforms, including Illumina, PacBio, and Oxford Nanopore. It can also simulate different types of sequencing errors, such as substitution, insertion, and deletion errors.
dwgsim: dwgsim is a short read simulator that can generate synthetic reads from whole genome sequencing data. It is designed to simulate reads from large genomes and can handle complex genome structures, such as translocations and inversions.
These are just a few examples of the many short read simulators available for bioinformatics research. The choice of the simulator depends on the specific research question and the type of sequencing technology used in the study.