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.