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Filters SPAdes output by coverage and length.

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CVLFilter

This is a python script that allows the user to filter SPAdes output fasta files by coverage or length.

To run: -On Windows machines, this script can be run by a double click. Otherwise, run the script using the command "python CVLFilter.py". Follow the prompts. -This can also be done directly using the following command: "python CVLFilter.py "

CVLplot

This is an R script that automatically generates coverage-versus-length plots for a scaffolds fasta file and outputs a list of the names of the scaffolds that pass the threshold and are to be kept. The current version of the script has been updated to take input.

To run:

-Open a command line window. -Type "Rscript CVLplotA.R <Length cutoff (in kb)> " and hit enter.

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Filters SPAdes output by coverage and length.

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  • R 75.3%
  • Python 24.7%