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pIRS specifications


Unique identifier OMICS_00254
Name pIRS
Alternative name profile based Illumina pair-end Reads Simulator
Software type Application/Script, Package/Module
Interface Command line interface
Restrictions to use None
Biological technology Illumina
Operating system Unix/Linux
Programming languages C++, Perl
License BSD 2-clause “Simplified” License, GNU General Public License version 2.0
Computer skills Advanced
Version 2.0.2
Stability Stable
Source code URL https://codeload.github.com/galaxy001/pirs/tar.gz/v2.0.2
Maintained Yes




No version available



  • person_outline Wei Fan

Publication for profile based Illumina pair-end Reads Simulator

pIRS citations


Evaluation of phylogenetic reconstruction methods using bacterial whole genomes: a simulation based study

Wellcome Open Res
PMCID: 5930550
PMID: 29774245
DOI: 10.21956/wellcomeopenres.15526.r32391

[…] resulting sequences of coding and non-coding regions at tips of the phylogeny while accounting for gene loss and transfer, and finally generated error prone Illumina reads from these sequences using pIRS v1.11 . An overview of this process is shown in ( ).To generate input to phylogenetic inference algorithms, we created assemblies and alignments from the simulated reads. We assembled the simula […]


A massively parallel strategy for STR marker development, capture, and genotyping

Nucleic Acids Res
PMCID: 5587753
PMID: 28666376
DOI: 10.1093/nar/gkx574

[…] t (similar to the requirements imposed for our analyses with real datasets) before calculation of performance metrics. In each of these simulations, Illumina short-read sequences were simulated using pIRs (). The average coverage of the sequences was varied between 5-fold to 39-fold, and BaitSTR was run using k-mer lengths between 9 and 31 bps for each of those coverage values. In each of those ru […]


Large scale genomic analysis shows no evidence for pathogen adaptation between the blood and cerebrospinal fluid niches during bacterial meningitis

Microb Genom
PMCID: 5361624
PMID: 28348877
DOI: 10.1099/mgen.0.000103

[…] the R6 and B6 reference sequences with progressive cactus []. A mean of 200 mutations with these rates was created in 100 sequences, and Illumina paired-end read data at 200× coverage simulated using pirs []. Variants between these sequences and a draft R6 assembly from simulated read data were then called using both of the above methods; comparison with the mutations known to be introduced allowe […]


GENE IS: Time Efficient and Accurate Analysis of Viral Integration Events in Large Scale Gene Therapy Data

Mol Ther Nucleic Acids
PMCID: 5363413
PMID: 28325279
DOI: 10.1016/j.omtn.2016.12.001

[…] xtracting 1,000 random sequences of 1 kb from the hg38 build. The vector was inserted at known genomic locations in the middle of each fragment. This library was used with a freely available program, profile-based Illumina pair-end Reads Simulator (pIRS), with default parameters to simulate four 100-bp sequencing datasets. Each dataset samples the library at four different coverage values: 1, 10, […]


Simulating Next Generation Sequencing Datasets from Empirical Mutation and Sequencing Models

PLoS One
PMCID: 5125660
PMID: 27893777
DOI: 10.1371/journal.pone.0167047

[…] %/2% of the average coverage). This is akin to the “ideal target” functionality of Wessim, and is likewise unrealistic.Our approach to quality score profiles is similar to Markov model approaches and pIRS (and earlier, MAQ), however we assume the quality score accurately represents the probability of erroneous base calls.Additionally, pIRS adjusts the likelihood of substitution vs. indel sequencin […]


AdapterRemoval v2: rapid adapter trimming, identification, and read merging

BMC Res Notes
PMCID: 4751634
PMID: 26868221
DOI: 10.1186/s13104-016-1900-2

[…] TP + FN) × (TN + FP) × (TN + FN)]}.We simulated 10 replications of 1 million 100 bp paired-end reads, with a mean insert size of 150 bp, and a standard deviation of 75 bp, using a modified version of pIRS v1.1.1 []. This version had been modified such that insert sizes less than the read length were allowed, and that adapter sequences were appended to such inserts prior to the simulation of read e […]


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pIRS institution(s)
BGI-Shenzhen, Shenzhen, China; Biodynamic Optical Imaging Center, Peking University, Beijing, China; Medical Population Genetics Program, Broad Institute, Cambridge, MA, USA
pIRS funding source(s)
Supported by Basic Research Program of Shenzhen City (grants JC2010526019); Key Laboratory Project of Shenzhen City (grants CXB200903110066A and CXB201108250096A); Shenzhen Key Laboratory of Gene Bank for National Life Science.

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