NANOPACK

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.