NEAT read simulation tools Long Description (required)
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. https://github.com/zstephens/neat-genreads zstephe2@illinois.edu
Step 1: Use the attribute tree to add new attributes or remove pre-selected attributes to describe the simulator.
Every sub-attribute is selected Not all sub-attributes are selectedFill Clear Expand Collapse Reset
Summary of Proposed Changes Step 2: Review list of proposed attribute addition(s) and subtraction(s).
Can't Find the Attribute You Are Looking For? If you would like to propose an attribute that you cannot find in the tree above, or if you would like to add a clarification to one or more attributes for this simulator (e.g. a specific file format for attribute /Output/File Format/Other), please list them in the Additional Comment box of the Submit tab .
Summary of Proposed Changes Current Citations/Applications
[Pubmed ID: 27893777 ],
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 ,
https://www.ncbi.nlm.nih.gov/pubmed/?term=27893777, Primary Citation
[Pubmed ID: 36496447 ],
Milhaven M, Pfeifer SP ,
Performance evaluation of six popular short-read simulators. ,
Heredity (Edinb) ,
02-01-2023 ,
https://www.ncbi.nlm.nih.gov/pubmed/?term=36496447, , Application
[Pubmed ID: 37389439 ],
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 ,
https://www.ncbi.nlm.nih.gov/pubmed/?term=37389439, , Application