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SimSeq specifications


Unique identifier OMICS_00258
Name SimSeq
Software type Package/Module
Interface Command line interface
Restrictions to use None
Biological technology Illumina, Life Technologies
Operating system Unix/Linux
Programming languages Java
License MIT License
Computer skills Advanced
Stability Stable
Maintained Yes


No version available


Publication for SimSeq

SimSeq citations


AMYCNE: Confident copy number assessment using whole genome sequencing data

PLoS One
PMCID: 5868770
PMID: 29579039
DOI: 10.1371/journal.pone.0189710

[…] The performance of AMYCNE was tested on a simulated WGS dataset consisting of 20 individuals carrying various mosaic aneuploidies of chromosome X. The simulation was done using Simseq ( and the detailed method used is given in (). The performance of AMYCNE was then compared to CNVnator as well as a simplistic method involving scaling of the […]


AIG1 affects in vitro and in vivo virulence in clinical isolates of Entamoeba histolytica

PLoS Pathog
PMCID: 5884625
PMID: 29554130
DOI: 10.1371/journal.ppat.1006882

[…] the genomes of E. histolytica, which were deposited into the GenBank database as follows. To construct simulated paired-end reads from the available genomic sequences of seven E. histolytica strains, SimSeq software [] was used with the following default parameter modifications: 14,000,000 paired-end reads, mean insert size of 200 mer, read length of 150 mer, and no mutations model. The short read […]


The Prevalence and Evolutionary Conservation of Inverted Repeats in Proteobacteria

Genome Biol Evol
PMCID: 5941160
PMID: 29608719
DOI: 10.1093/gbe/evy044

[…] Sequences were simulated along rooted phylogenetic trees using the module Simseq of the R package phangorn V2.2.0 (). Each IR and each control sequence were simulated according to the phylogenetic tree using the inferred evolutionary model parameters in the region in which […]


EAMA: Empirically adjusted meta analysis for large scale simultaneous hypothesis testing in genomic experiments

PLoS One
PMCID: 5663489
PMID: 29088275
DOI: 10.1371/journal.pone.0187287

[…] We also generated realistic NGS-like datasets for our simulation experiments using a popular NGS-simulator called SimSeq []. SimSeq generates read counts in two treatment groups for a known set of differentially expressed genes based on a real RNA-sequencing dataset. Here, we generated a count data using SimSeq a […]


More on the Best Evolutionary Rate for Phylogenetic Analysis

Syst Biol
PMCID: 5790136
PMID: 28595363
DOI: 10.1093/sysbio/syx051

[…] We simulated nucleotide sequences on the simulated trees using the simSeq function in the “phangorn” package in R (). A range of evolutionary rates was examined from 0.025 to 10 expected substitutions from root to any tip. In the most basic setup, we simulated sequen […]


Positional bias in variant calls against draft reference assemblies

BMC Genomics
PMCID: 5368935
PMID: 28351369
DOI: 10.1186/s12864-017-3637-2

[…] Sequences for chromosomes 1 and 2 of Arabidopsis thaliana (TAIR10) were downloaded from The Arabidopsis Information Resource website [].To simulate the reads we used SimSeq application that aims to reproduce the biases present in normal Illumina data sets []. We ran the application with default parameters to simulate 15 mln 100 bp paired-end reads with the mean in […]

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SimSeq institution(s)
Center for Biomolecular Science and Engineering, University of California, Santa Cruz, CA, USA

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