BSD Ports

wip/nanomath 1.2.1.20210604 NetBSD

Math functions for other Oxford Nanopore processing scripts

System
NetBSD
Repository
pkgsrc-wip
Maintainer
[email protected]
License
gnu-gpl-v3
Categories
wip, biology, python

Description

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)`

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

Install

From pkgsrc-wip (no binary package):

cd /usr/pkgsrc/wip/nanomath && make install clean

Dependencies

Run dependencies 2