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Citations per year

Number of citations per year for the bioinformatics software tool ReadSim

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ReadSim specifications


Unique identifier OMICS_12445
Name ReadSim
Software type Package/Module
Interface Command line interface
Restrictions to use None
Biological technology Pacific Biosciences, Oxford Nanopore
Operating system Unix/Linux, Mac OS, Windows
Programming languages Python
Computer skills Advanced
Version 1.6
Stability Stable
Maintained Yes


No version available


  • person_outline Michael Schatz

Publication for ReadSim

ReadSim citations


Assessment of Metagenomic Assembly Using Simulated Next Generation Sequencing Data

PLoS One
PMCID: 3285633
PMID: 22384016
DOI: 10.1371/journal.pone.0031386

[…] hod and the amount of sequencing (number of reads) have to be specified. Using these parameters the simulator calculates how many reads of each organism's genome should be sequenced. iMESS then calls ReadSim ( to generate reads with sequencing errors but without quality values. Quality value models were determined by obtaining quality values from ac […]


Integrating Sequencing Technologies in Personal Genomics: Optimal Low Cost Reconstruction of Structural Variants

PLoS Comput Biol
PMCID: 2700963
PMID: 19593373
DOI: 10.1371/journal.pcbi.1000432

[…] llumina) sequencing, were considered with the characteristics summarized in . We also assumed that the per-base sequencing error rate increases linearly from the start to the end of a read similar to ReadSim , and assigned error types (insertion, deletion or substitution) randomly according to the characteristics of the sequencing technique used ,,. The novel SVs used in the novel insertion recons […]


Viral Population Estimation Using Pyrosequencing

PLoS Comput Biol
PMCID: 2323617
PMID: 18437230
DOI: 10.1371/journal.pcbi.1000074

[…] these three steps.The simulations show that Algorithm 1 reduces the error rate by a factor of 30. This performance is largely independent of the number of haplotypes in the population (). The program ReadSim was used to simulate the error process of pyrosequencing. The error rate after alignment is about 1 to 3 errors per kb, so we are left with about 0.1 errors per kb after error correction. As […]

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ReadSim institution(s)
Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA; Department of Computer Science, Stony Brook University, Stony Brook, NY, USA; Department of Computer Science, Columbia University, New York, NY, USA; Computational Science Center, Brookhaven National Laboratory, NY, USA; Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA

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