nanomath - DEPRECATED

AS OF 2024-06-20, THIS REPOSITORY IS DEPRECATED. ITS CODE IS INTEGRATED INTO NANOPLOT.

This module provides a few simple math and statistics functions for other scripts processing Oxford Nanopore sequencing data

FUNCTIONS

• Calculate read N50 from a set of lengths get_N50(readlenghts)
• Remove extreme length outliers from a dataset remove_length_outliers(dataframe, columname)
• Calculate the average Phred quality of a read ave_qual(qualscores)
• Write out the statistics report after calling readstats function write_stats(dataframe, outputname)
• Compute a number of statistics, return a dictionary calc_read_stats(dataframe)

As of v1.3.0, nanomath calculates the average quality differently, by first converting per-read phred scale averages to error rates, take the average, and converting back (nanostat#40)

INSTALLATION

pip install nanomath

or

conda install -c bioconda nanomath

CONTRIBUTORS

@alexomics for fixing the indentation of the printed stats

CITATION

If you use this tool, please consider citing our publication.