GSR: Simulator - GemSIM
Attribute | Value |
---|---|
Title | GemSIM |
Short Description | Next generation sequencing read simulator |
Long Description | GemSIM is a software package for generating realistic simulated next generation sequencing reads with quality score values. Both Illumina and Roche/454 reads (single or paired end) can be simulated using empirically derived error models. |
Version | 1.6 |
Project Started | 2013 |
Last Release | 11 years ago |
Homepage | http://sourceforge.net/projects/gemsim/ |
Citations | McElroy KE, Luciani F, Thomas T, GemSIM: general, error-model based simulator of next-generation sequencing data., BMC Genomics, 02-15-2012 [ Abstract, cited in PMC ] |
GSR Certification | ✔ Accessibility |
Last evaluated | 06-13-2019 (1766 days ago) |
Attribute Category | Attribute |
---|---|
Target | |
Type of Simulated Data | Diploid DNA Sequence, Haploid DNA Sequence, Mitochondrial DNA, Sequencing Reads, |
Variations | Single Nucleotide Variation, Insertion and Deletion, Inversion and Rearrangement, Genotype or Sequencing Error, Other, |
Simulation Method | Other, |
Input | |
Data Type | Other, |
File format | Other, |
Output | |
Data Type | Genotype or Sequence, |
Sequencing Reads | Other, |
File Format | Fasta or Fastq, |
Sample Type | Other, |
Phenotype | |
Trait Type | |
Determinants | |
Evolutionary Features | |
Demographic | |
Population Size Changes | |
Gene Flow | |
Spatiality | |
Life Cycle | |
Mating System | |
Fecundity | |
Natural Selection | |
Determinant | |
Models | |
Recombination | |
Mutation Models | |
Events Allowed | |
Other | Phenogenetic, Polygenic background, |
Interface | Command-line, |
Development | |
Tested Platforms | Mac OS X, Linux and Unix, |
Language | Python, |
License | GNU Public License, |
GSR Certification | Accessibility, Documentation, Application, |
Number of Primary Citations: 1
Number of Non-Primary Citations: 2
The following 2 publications are selected examples of applications that used GemSIM.
2023
Zachariasen T, Petersen AØ, Brejnrod A, Vestergaard GA, Eklund A, Nielsen HB, Identification of representative species-specific genes for abundance measurements., Bioinform Adv, 05-08-2023 [Abstract]
2021
Tang K, Wang W, Sun Y, Zhou Y, Wang P, Guo Y, Wang X, Prophage Tracer: precisely tracing prophages in prokaryotic genomes using overlapping split-read alignment., Nucleic Acids Res, 12-16-2021 [Abstract]