BSD Ports

wip/nanopack 0.0.0.20210524 NetBSD

Long read processing and analysis scripts

System
NetBSD
Repository
pkgsrc-wip
Maintainer
[email protected]
Categories
wip, meta-pkgs, biology

Description

This is a meta package that depends on all components of NanoPack.

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

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.

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.

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.

Install

From pkgsrc-wip (no binary package):

cd /usr/pkgsrc/wip/nanopack && make install clean

Dependencies

Run dependencies 6

No port depends on this one.