Genome Assembly Stats

Python script for summarizing a genome assembly

This script will summaryze the nucleotide content in a fasta file by calculating:

Total sequences
Total bases
Total Ns (undefined bases)
Total Gaps (strings of undefined bases longer than 5)
Shortest sequence
Longest sequence
Mean length
N50
Overall G+C content
Min G+C per sequence
Max G+C per sequence

Running the script with test files

Before running the script, make sure the following libraries are installed (tested in Python 3.8.12, macOS Big Sur):

import tabulate
import plotext as plt

Results are also printed on the screen, make sure you're using a suitable python version.

python fastaMetrics_py3.py -h 
usage: fastaMetrics.py [-h] -i INPUT -o OUTPUT

Calculate summary statistics for genome assemblies
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Tested in python 3.8.12

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

Mandatory arguments:
  -i INPUT, --input, Input fasta file (genome assembly)
  -o OUTPUT, --output, Prefix for the output files, results are also printed on screeen

Running script with test file:

python fastaMetrics_py3.py -i pfalciparium3D7_PlasmoDB-61.fasta -o pf3d7

Output

Results are also saved in a tsv file, as shown in the figure above (pf3d7_Summary.txt). It will also produce a table containing the cumulative length (pf3d7_CumulativeLength.txt).