assembly_stats

A Python library that takes a FASTA file as input and calculates both scaffold and contig statistics (N50, L50, etc.) from a scaffold FASTA file. It does this by breaking each scaffold wherever there is more than one N and then calculating statistics for both the scaffolds and contigs.

This is a re-write of fasta_metadata_parser to speed up the old implementation, and -- most importantly -- to learn how to install Python scripts onto the Smithsonian HPC.

Installation

pip install assembly_stats

Usage

  $ assembly_stats -h

    usage: assembly_stats [-h] filename

    Calculate statistics about genome assemblies.

    positional arguments:
      filename    Genome file in FASTA format.

    optional arguments:
      -h, --help  show this help message and exit

After calculating the statistics for the genome assembly, they will be printed out in JSON format.

Next steps

• Add ability to save NumPy sequence length arrays for further visualization, since generating these are what takes the most time.