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.
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
get_N50(readlenghts)remove_length_outliers(dataframe, columname)ave_qual(qualscores)write_stats(dataframe, outputname)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
or
CONTRIBUTORS
@alexomics for fixing the indentation of the printed stats
CITATION
If you use this tool, please consider citing our publication.