https://github.com/ahcm/longread_plots
A collection of plots for long read sequencing FastQ files from devices like Oxford Nanopore's MinION and PromethION.
https://github.com/ahcm/longread_plots
fastq longread nanopore plot qualitycontrol
Last synced: 5 months ago
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A collection of plots for long read sequencing FastQ files from devices like Oxford Nanopore's MinION and PromethION.
- Host: GitHub
- URL: https://github.com/ahcm/longread_plots
- Owner: ahcm
- License: bsd-2-clause
- Created: 2018-05-24T08:51:10.000Z (about 8 years ago)
- Default Branch: master
- Last Pushed: 2023-02-14T10:27:27.000Z (over 3 years ago)
- Last Synced: 2025-10-27T07:49:57.840Z (8 months ago)
- Topics: fastq, longread, nanopore, plot, qualitycontrol
- Language: Python
- Homepage:
- Size: 593 KB
- Stars: 12
- Watchers: 1
- Forks: 0
- Open Issues: 1
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# longread_plots
A collection of plots for long read sequencing FastQ files from devices like Oxford Nanopore's MinION and PromethION.
# Dependencies
```bash
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:
```bash
pip3 install --user lrplots
```
From the release tar.gz:
```bash
python3 setup.py install --user
```
# Usage
With the pip3 installation it should be in your PATH and you should be able to just call:
```bash
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:
```bash
find ~ -name lrplot
```
or
```bash
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):
```bash
python3 bin/lrplots example.fastq
```
# Output
