NEAT-genreads

NEAT-genreads or the NEAT project NExt-generation sequencing Analysis Toolkit is a software tool package to simulate sequenced reads based on specific datasets. The NEAT can produce, e.g., whole genomes, target specific regions, insert sequence variants, and large single-end reads. The NEAT package includes the following utilities: computeGC.py, computeFraglen.py, genMutModel.py, genSeqErrorModel.py, and plotMutModel.py.

Topic

Simulation experiment;Sequence sites, features and motifs

Detail

  • Operation: Modelling and simulation;Random sequence generation

  • Software interface: Command-line user interface

  • Language: Python 3

  • License: BSD 3-Clause

  • Cost: Free

  • Version name: 3.2

  • Credit: NSF.

  • Input: FASTA

  • Output: simulated_data

  • Contact: zstephe2@illinois.edu

  • Collection: -

  • Maturity: Emerging/Stable

Publications

  • Simulating Next-Generation Sequencing Datasets from Empirical Mutation and Sequencing Models.
  • 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. 2016 Nov 28;11(11):e0167047.
  • https://doi.org/10.1371/journal.pone.0167047
  • PMID: 27893777
  • PMC: PMC5125660

Download and documentation

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