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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.

Installation

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

Content

Scripts

`NanoPlot <https://github.com/wdecoster/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 <https://github.com/wdecoster/nanogui>`__.

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

`NanoStat <https://github.com/wdecoster/nanostat>`__: Quickly create a statistical summary from reads, an alignment or a summary file.

`NanoFilt <https://github.com/wdecoster/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 <https://github.com/wdecoster/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 <https://github.com/wdecoster/nanoget>`__: Functions for extracting features from reads, alignments and albacore summary data, parallelized.

`nanomath <https://github.com/wdecoster/nanomath>`__: Functions for mathematical processing and calculating statistics.

`nanoplotter <https://github.com/wdecoster/nanoplotter>`__: Appropriate plotting functions, building on the seaborn module.

Test data

`nanotest <https://github.com/wdecoster/nanotest>`__ provides small test datasets in fastq, bam and summary format (not included when installing NanoPack)

Project details


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