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Install all Oxford Nanopore scrips and modules for processing and analysis

Project description

Easily install all my long read processing and analysis scripts simultaneously.


pip install nanopack ## Updating pip install nanopack --upgrade



`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 <>`__.

`NanoComp <>`__: comparing multiple runs on read length and quality based on reads (fastq), alignments (bam) or albacore summary files.

`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 and minimum quality cut-off. 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.


`nanoget <>`__: Functions for extracting features from reads, alignments and albacore summary data, parallelized.

`nanomath <>`__: Functions for mathematical processing and calculating statistics.

`nanoplotter <>`__: Appropriate plotting functions, building on the seaborn module.

Test data

`nanotest <>`__ provides small test datasets in fastq, bam and summary format (not included when installing NanoPack)

Project details

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