wip/nanostat 1.5.0.20210108 NetBSD

Statistics for Oxford Nanopore sequencing data and alignments

System: NetBSD
Repository: pkgsrc-wip
Maintainer: [email protected]
License: gnu-gpl-v3
Categories: wip, biology, python

Description

# NanoStat

Calculate various statistics from a long read sequencing dataset in fastq, bam or albacore sequencing summary format.

#### Examples

NanoStat --fastq reads.fastq.gz --outdir statreports

NanoStat --summary sequencing_summary1.txt sequencing_summary2.txt \ sequencing_summary3.txt --readtype 1D2

NanoStat --bam alignment.bam alignment2.bam

I welcome all suggestions, bug reports, feature requests and contributions. Please leave an issue (https://github.com/wdecoster/nanostat/issues) or open a pull request.

If you use this tool, please consider citing our publication: https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/bty149/4934939.

Install

From pkgsrc-wip (no binary package):

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

Dependency graph

Ports that need it on the left, what it needs to run on the right; at most 8 of each. "Dependencies" below lists them all.

graph LR
  me["wip/nanostat"]
  u0["wip/nanopack"] --> me
  me --> d0["biology/htslib"]
  me --> d1["devel/py-deprecated"]
  me --> d2["wip/nanoget"]
  me --> d3["wip/nanomath"]
  me --> d4["wip/py-pysam"]
  classDef this fill:#ab2b28,color:#ffffff,stroke:#ab2b28
  class me this

Dependencies

Run dependencies 5

Required by 1

wip/nanopack