rnaQUASTcompare

Small python command line tool that generates comparative plots for multiple rnaQUAST short reports.

rnaQUAST (https://github.com/ablab/rnaquast) is a great tool for the evaluation of transcriptome assemblies. It generates a multitude of metrics for the quality of transcriptome assemblies, many of them by mapping the transcripts to an annotated genome. rnaQUAST does a great job at rating individual assemblies, however, directly comparing different reports is not as easy.

This tool merges multiple rnaQUAST short reports into a single dataframe which is outputted in TSV, CSV and TEX and compiled into an easy to interpret plot.

rnaQUASTcompare converts mismatches per transcript to mismatches per (aligned) kilo base to not favour assemblies with shorter transcripts.

usage: rnaQUASTcompare [-h] [-n  [...]] [-c  [...]] [-t] [-o] report_dirs [report_dirs ...]

Comparing rnaQUAST reports from multiple assemblies. Generates combined Dataframes (.csv, tsv and .tex) and plots.

positional arguments:
  report_dirs           paths to output directories from rnaQUAST

options:
  -h, --help            show this help message and exit
  -n  [ ...], --names  [ ...]
                        list of names for the assemblies (default=["auto"])
  -c  [ ...], --colors  [ ...]
                        list of colors in hexcode (default=["auto"])
  -t , --title          main title for plot

Exemplary output