Calculates both scaffold and contig statistics (N50, L50, etc.) from a scaffold FASTA file.
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.
pip install assembly_stats
$ 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.
- Add ability to save NumPy sequence length arrays for further visualization, since generating these are what takes the most time.
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