/Nchart

Creates an N-chart for comparing assembly lengths, including script for counting assembly lengths from a fasta file

Primary LanguageR

N-chart

Example Nchart

Directions:

  1. Install fastalengths by running chmod +x fastalengths and adding it to a bin in your path, such as /usr/local/bin/

  2. Run fastalengths on each of your assemblies and your reference genome:

    fastalengths my_assembly.fasta > my_assembly.fasta.lengths

    Or with a quick loop in bash:

    for f in *.fa; do fastalengths $f > $f.lengths; done

  3. Edit the first few lines of Nchart_script.R with your filenames (the .lengths files) and nicknames for the assemblies you wish to compare, then run it.