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V-Z edited this page Dec 18, 2017 · 26 revisions

Sondovač is a script to create orthologous low-copy nuclear probes from transcriptome and genome skim data for target enrichment.

When using Sondovač, please cite Schmickl et al. 2016: Phylogenetic marker development for target enrichment from transcriptome and genome skim data: the pipeline and its application in southern African Oxalis (Oxalidaceae) in Molecular Ecology Resources; DOI: 10.1111/1755-0998.12487.

Sondovač is written primarily in BASH, so that it is portable among operating systems (any UNIX-based operating system - Linux, Mac OS X and more - is equipped with BASH, and it can be installed into Windows), although only selected Linux distributions and Mac OS X are fully tested and supported.

How to obtain Sondovač

  • GitHub repository contains only basic scripts, not all files needed to run Sondovač - get the latest release containing also all needed binaries and 3rd party software.
  • Currently, the latest release is v1.3.
  • Get separate package with sample data.
  • See documentation for information about installation and usage of Sondovač.

Notes

  • In case of problems, requests, questions, feel free to open new issue.
  • Sondovač is currently tested on major Linux distributions and Mac OS X (see README or manual for details). Anyway, you can run it on any UNIX-based operating system.

Sondovač is a script to create orthologous low-copy nuclear probes from transcriptome and genome skim data for target enrichment. When using Sondovač, please, cite Schmickl et al 2016. Wiki home.

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