Benchmark 2#

All shell command blocks begin at the folder root: benchmark_2


benchmark_2 is the benchmark presented at:

  • WABI 2022

Data format#

NODE line#

NODE   node_name   contig_name   multiplicity   X_coord   Y_coord
  • node_name in the graph, a contig is represented by 2 nodes : contig_name_L and contig_name_R

  • contig_name name of the contig

  • multiplicity number of occurrence of the contigs

    • x = don’t know

    • * = zero or more

    • 1 = one or more

    • s = one or more (start contig)

    • 1, 2, 3, ... exact number of occurrences

  • X_coord X coordinate used for the graphic representation

  • Y_coord Y coordinate used for the graphic representation

CONTIG line#

CONTIG  name  coverage   sequence
  • name name of the contig

  • coverage average coverage of the contig

  • sequence ATGC string of the contig

Install & configurations#

1. Python environment#

  • You need to install virtualenv

    pip install virtualenv
  • Create python virtual environment

  • Activate the environment

    source .venv_39/bin/activate

Always make sure the environment is activated!

(.venv_39) # command lines may be prefix by the environment name


QUAST is used to evaluate the scaffolding (and the pre-assembly).

One fix is automatically done in .venv_39/lib/python3.9/site-packages/quast_libs/site_packages/jsontemplate/

  • replacing import cgi by import html \((\times 1)\)

  • replacing all cgi.escape by html.escape \((\times 6)\)

see issue 157

sed -i 's/cgi/html/' .venv_39/lib/python3.9/site-packages/> quast_libs/site_packages/jsontemplate/


  • source the environment

    source .venv_39/bin/activate
  • run the benchmark

    python3.9 scripts/  # [-h] see help
  • run QUAST evaluation

    python3.9 scripts/ -d run/...  # [-h] see help
  • extract stats in a tex table (e.g. for WABI2022 conference)

    python3.9 scripts/ -d run/...  # [-h] see help
  • generate figures with R

    Rscript scripts/make_fig.R run/...  # [-h] see help


  • remove quast directories in run/...

    find . -maxdepth 2 -type d -name 'quast' | xargs rm -rf