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 <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>`__ or as a `web service <http://nanoplot.bioinf.be>`__.
`NanoComp <https://github.com/wdecoster/nanocomp>`__: comparing multiple runs on read length and quality based on reads (fastq), alignments (bam) or albacore summary files.
`NanoQC <https://github.com/wdecoster/nanoQC>`__: Generating plots to investigate nucleotide composition and quality distribution at the end of reads.
`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, minimum quality cut-off, minimum and maximum average GC. 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.
Test data
`nanotest <https://github.com/wdecoster/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.
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