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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

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


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Files for nanopack, version 1.1.0
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