Install all Oxford Nanopore scrips and modules for processing and analysis
Project description
Easily install all my long read processing and analysis scripts simultaneously.
Installation
pip install nanopack ## Updating pip install nanopack --upgrade
These scripts are written and tested for Python3, and may not work on Python2.
Content
Scripts
NanoPlot: creating many relevant plots derived from reads (fastq), alignments (bam) and albacore summary files. Examples can be found in the gallery on my blog. NanoPack is also available with a graphical user interface in NanoGUI or as a web service.
NanoComp: comparing multiple runs on read length and quality based on reads (fastq), alignments (bam) or albacore summary files.
NanoQC: Generating plots to investigate nucleotide composition and quality distribution at the end of reads.
NanoStat: Quickly create a statistical summary from reads, an alignment or a summary file.
NanoFilt: Streaming script for filtering a fastq file based on a minimum length, minimum quality cut-off, minimum and maximum average GC. Also trimming nucleotides from either read ends is an option.
NanoLyse: Streaming script for filtering a fastq file to remove reads mapping to the lambda phage genome (control DNA used in nanopore sequencing). Uses minimap2/mappy.
Modules
nanoget: Functions for extracting features from reads, alignments and albacore summary data, parallelized.
nanomath: Functions for mathematical processing and calculating statistics.
Test data
nanotest provides small test datasets in fastq, bam and summary format (not included when installing NanoPack)
## CITATION If you use this tool, please consider citing our publication.
Project details
Release history Release notifications | RSS feed
Download files
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.