Chromatogram File Utils

DNA, mutation, chromatogram, biology, bioinformatics, mutations, sanger-chromatograms
pip install cfutils==0.0.0.dev52


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Chromatogram File Utils

For Sanger sequencing data visualizing, alignment, mutation calling, and trimming etc.


plot chromatogram with mutation

command to generate the demo above

cfutils mut --query ./data/B5-M13R_B07.ab1 --subject ./data/ref.fa --outdir ./data/ --plot

How to install?

form pypi

(use this way ONLY, if you don't know what's going on)

pip install --user cfutils

manipulate the source code

  • clone from github
git clone
  • install the dependence
make init
  • do unittest
make test

How to use?

  • in the command line
cfutils mut --help
  • or as a python module
import cfutils as cf


  • build as python package for pypi
  • fix bug that highlighting wrong base
  • replace blastn with buildin python aligner


  • call mutation by alignment and plot Chromatogram graphic

  • add a doc

  • change xaxis by peak location

  • fix bug that chromatogram switch pos after trim

  • wrap as a cli app

  • return quality score in output

  • fix issue that selected base is not in the middle

  • fix plot_chromatograph rendering bug

  • add projection feature to make align and assemble possible