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ConSequences

ConSequences is an R script designed to perform semi-automatic curation of NCBI GenBank data. The data after curation with ConSequences is ready for analysis in Modeltest-NG and RAxML-NG.

Functions available in ConSequences script:

  • change.seq.names - automatically changes sequences names based on their accession numbers, when a table of sequence metadata is provided (see an examplary sequence metadata table - Umbelopsis.csv)
  • fill.with.pluses - fills the missing molecular marker data for each strain with pluses based on a table of sequence metadata
  • concatenate.sequences - concatenates molecular data for each strain

Functions change.seq.names and concatenate.sequences perform additional verification of your data. They print a report if the sequences data or metadata table are incomplete.

Additional information about functions usage and the code can be found in ConSequences.R file.

Files

ConSequences.R - contains thoroughly described script with functions for data curation, an examplary code to use with a test data provided and author's data necessary for citation.

Test - folder containing test data:

  • Umbelopsis.csv - an examplary table containing sequence metadata to use with the test data
  • act1.txt, COI.txt, ITS.txt, LSU.txt, mcm7.txt, SSU.txt - an examplary accession numbers files used to download test data via BatchEntrez on the GenBank website.

Citation

If You use this code in Your work, please cite this repository along with the script name. Author's data necessary for citation are available in ConSequences.R file.