longread_plots

A collection of plots for long read sequencing FastQ files from devices like Oxford Nanopore's MinION and PromethION.

Dependencies

pip install --user --upgrade pandas seaborn

Note that matplot lib >= 3.0.0 is needed and 3.6.1 has a breaking bug (3.6.2 on are fine). Python >= 3.5 is therfore recommended, otherwise plots might be corrupted.

Speed up with lrdf

The aggregation of the data in python is quite slow. Therefore I implemented it as a standalone rust implementation, which can be found here: https://github.com/ahcm/lrdf

Installation

From PyPi:

pip3 install --user lrplots

From the release tar.gz:

python3 setup.py install --user

Usage

With the pip3 installation it should be in your PATH and you should be able to just call:

lrplot example.fastq

If the command can't be found, pip3 installed it in a path that is not in your PATH variable. You can then find it with:

find ~ -name lrplot

or

find /usr/local -name lrplot

Then either add the containing directory to your PATH or just use the full path.

You can also call it like a script with python3 (or whatever your python3 is called):

python3 bin/lrplots example.fastq

Output