nanomath 1.4.0

A few simple math function for other Oxford Nanopore processing scripts

# nanomath

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

[](https://twitter.com/wouter_decoster) [](https://anaconda.org/bioconda/nanomath) [](https://tracker.debian.org/pkg/python-nanomath)

## 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](<https://github.com/wdecoster/nanostat/issues/40>))

## INSTALLATION

`bash pip install nanomath `

or [](https://anaconda.org/bioconda/nanomath)

` conda install -c bioconda nanomath `

## CONTRIBUTORS

[@alexomics](https://github.com/alexomics) for fixing the indentation of the printed stats

## CITATION

If you use this tool, please consider citing our [publication](https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/bty149/4934939).