GSR: Simulator - NEAT
Attribute | Value |
---|---|
Title | NEAT |
Short Description | NEAT read simulation tools |
Long Description | NEAT-genReads is a fine-grained read simulator. GenReads simulates real-looking data using models learned from specific datasets. There are several supporting utilities for generating models used for simulation. |
Version | 2.0 |
Project Started | 2016 |
Last Release | 7 years, 5 months ago |
Homepage | https://github.com/zstephens/neat-genreads |
Citations | Stephens ZD, Hudson ME, Mainzer LS, Taschuk M, Weber MR, Iyer RK, Simulating Next-Generation Sequencing Datasets from Empirical Mutation and Sequencing Models., PLoS One, 01-01-2016 [ Abstract, cited in PMC ] |
GSR Certification | ✔ Accessibility |
Last evaluated | 05-30-2018 (2145 days ago) |
Author verification | The basic description provided was derived from a website or publications by the GSR team and has not yet been verified by the simulation author. To modify this entry or add more information, propose changes to this simulator. |
Attribute Category | Attribute |
---|---|
Target | |
Type of Simulated Data | Sequencing Reads, |
Variations | Biallelic Marker, Multiallelic Marker, Single Nucleotide Variation, Insertion and Deletion, |
Simulation Method | Resample Existing Data, Other, |
Input | |
Data Type | Reference genome, |
File format | Other, |
Output | |
Data Type | |
Sequencing Reads | Illumina, |
File Format | Fasta or Fastq, |
Sample Type | |
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 | |
Interface | Command-line, |
Development | |
Tested Platforms | Windows, Mac OS X, Linux and Unix, |
Language | Python, |
License | Other, |
GSR Certification | Accessibility, Documentation, Application, Support, |
Number of Primary Citations: 1
Number of Non-Primary Citations: 2
The following 2 publications are selected examples of applications that used NEAT.
2023
Milhaven M, Pfeifer SP, Performance evaluation of six popular short-read simulators., Heredity (Edinb), 02-01-2023 [Abstract]
Roder AE, Johnson KEE, Knoll M, Khalfan M, Wang B, Schultz-Cherry S, Banakis S, Kreitman A, Mederos C, Youn JH, et al., Optimized quantification of intra-host viral diversity in SARS-CoV-2 and influenza virus sequence data., mBio, 08-31-2023 [Abstract]