Assembly Metrics Toolkit

Prerequisite

• Perl
  • Cpanm
• Python 2.7 or 3.5

Installation

cpanm --installdeps .

Usage

usage: python assembly_metrics_toolkit.py [-h] [-s scaffolds_file]
[-c contigs_file] [-o output_path]

Calculate various assembly metrics

optional arguments:
  -h, --help         show this help message and exit
  -s scaffolds_file  a fasta file of scaffolds (can be .gz)
  -c contigs_file    a fasta file of contigs (can be .gz)
  -o output_path     where a JSON output file will be generated at

Example

Download the example files

We are using the scaffolds and contigs of Athalia rosae provided by i5k Workspace@NAl.

wget "https://i5k.nal.usda.gov/data/Arthropoda/athros-(Athalia_rosae)/BCM-After-Atlas/1.Genome%20Assembly/BCM-After-Atlas/Contigs/Aros01112013-contigs.fa.gz"
wget "https://i5k.nal.usda.gov/data/Arthropoda/athros-(Athalia_rosae)/BCM-After-Atlas/1.Genome%20Assembly/BCM-After-Atlas/Scaffolds/Aros01112013-genome.fa.gz"

Run the script

python ./assembly_metrics_toolkit.py -s ./Aros01112013-genome.fa.gz -o example_scaffolds_only.json
python ./assembly_metrics_toolkit.py -s ./Aros01112013-genome.fa.gz -c ./Aros01112013-contigs.fa.gz -o example_scaffolds_and_contigs.json

These commands will generate two json files, which are the same as example_scaffolds_only.json and example_scaffolds_and_contigs.json, respectively.

These json files can be further visualized through Assembly_Metrics_Visualization.

Acknowledgement

• assemblathon_stats.pl and FAlite.pm are from ucdavis-bioinformatics/assemblathon2-analysis GitHub Repo.
• asm2stats.minmaxgc.pl is from rjchallis/assembly-stats GitHub Repo, and is modified to also support .gz input fasta file.