nanopack 0.1.0

Install all Oxford Nanopore scrips and modules for processing and analysis

Easily install all my Oxford Nanopore processing and analysis scripts at the same time.

Installation

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

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.

`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.

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

`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.

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

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