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Merly Escalona edited this page Sep 27, 2017 · 22 revisions

NGSphy is a Python open-source tool for the genome-wide simulation of NGS data (read counts or Illumina reads) obtained from thousands of gene families evolving under a common species tree, with multiple haploid and/or diploid individuals per species, where sequencing coverage (depth) heterogeneity can vary among species, individuals and loci, including off-target and untargeted loci.

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Wiki

Getting started

Full Manual

  1. About NGSphy
  2. Citation
  3. Input/output files
  4. NGS overage heterogeneity
  5. Installation
    1. Computer requirements
    2. NGSphy
    3. Third-party software
    4. Adding NGSphy and third-party software to the path
  6. Usage
  7. The settings file
    1. general block
    2. data block
    3. coverage block
    4. ngs reads art block
    5. ngs read counts block
    6. execution block
  8. Output
    1. Alignments
    2. Coverage
    3. Ind_labels
    4. Individuals
    5. Ref_alleles
    6. Scripts
    7. NGS mode
    8. Other files
  9. Additional information
    1. Motivation
    2. What can be done with NGSphy?
    3. Third-party software involved
    4. NGSphy workflow
    5. Read count simulation
  10. Getting help
  11. References

Older versions of the manual

Validation test

Use case test

Tutorials

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