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


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  • person_outline Michael Schatz <>

Publication for ReadSim

ReadSim in publications

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

[…] 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 […]

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

[…] 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. […]

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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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