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nasp

Northern Arizona SNP Pipeline

https://github.com/tgennorth/nasp

Science Score: 23.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ○
    codemeta.json file
  • ○
    .zenodo.json file
  • ✓
    DOI references
    Found 2 DOI reference(s) in README
  • ○
    Academic publication links
  • ✓
    Committers with academic emails
    1 of 13 committers (7.7%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (16.3%) to scientific vocabulary
Last synced: 11 months ago · JSON representation

Repository

Northern Arizona SNP Pipeline

Basic Info
  • Host: GitHub
  • Owner: TGenNorth
  • License: other
  • Language: Python
  • Default Branch: master
  • Homepage: TGenNorth.github.io/NASP
  • Size: 82.6 MB
Statistics
  • Stars: 19
  • Watchers: 12
  • Forks: 8
  • Open Issues: 6
  • Releases: 0
Created about 13 years ago · Last pushed over 1 year ago
Metadata Files
Readme Changelog Contributing License

README.rst 

.. image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat-square
    :target: http://bioconda.github.io/recipes/nasp/README.html
    :alt: install with bioconda

.. image:: https://landscape.io/github/TGenNorth/NASP/tests/landscape.svg?style=flat
   :target: https://landscape.io/github/TGenNorth/NASP/tests
   :alt: Code Health

.. |copy|   unicode:: U+000A9 .. COPYRIGHT SIGN

The Northern Arizona SNP Pipeline (NASP)
========================================

ANNOUNCEMENT:
---------

As of NOV 2022, The Northern Arizona Pipeline is currently being revised and will be updated. The current release version (https://github.com/TGenNorth/NASP/releases/tag/v1.2.0) will not recieve further updates but will continue to be supported until the release of the upcoming version. Stay tuned for further updates on development.

OVERVIEW:
---------

NASP is a pipeline for analysis of genomic data. It is a suite of tools
meant to collect and report on statistically-relevant high-confidence
positions in a collection of genomes, with emphasis on variant
positions, especially single nucleotide polymorphisms (SNPs). NASP
expects some combination of files in FASTA, FASTQ, SAM, BAM, and VCF
format as input, and will produce output files also in
those formats. As NASP is a pipeline, it expects to link a set of
external tools (usually installed separately) to complete specific
analysis tasks.

USAGE:
------

Usage depends upon the installation method used on your system, and the
user interface you select. For standard installations with the
command-line interface, you would collect (or symbolically link) all of
your input files into a folder, and then invoke the command-line
interface from that folder. Expected usage for the command-line
interface is:

`nasp.py [output\_folder]`

You will then be prompted to answer a few questions about your analysis.

Optionally, if you are re-running a previous analysis with the same (or
similar) options, you can pass in an xml-based configuration file (this
is written out to your output\_folder after running the command-line
interface) using the format:

`nasp.py --config`

INSTALLATION:
-------------

See the main page for documentation (http://tgennorth.github.io/NASP/).

DEPENDENCIES:
-------------

For information about external tools that are required, or can be
utilized, and those versions that have been tested to work with NASP,
refer to the main NASP page (http://tgennorth.github.io/NASP/)

LICENSE:
--------

Copyright |copy| The Translational Genomics Research Institute See the
included "LICENSE" document.

PUBLICATION:
--------

Please read our paper for more information:

Jason W. Sahl,  Darrin Lemmer,  Jason Travis,  James M. Schupp,  John D. Gillece,  Maliha Aziz,  Elizabeth M. Driebe,  Kevin P. Drees,  Nathan D. Hicks,  Charles Hall Davis Williamson,  Crystal M. Hepp,  David Earl Smith,  Chandler Roe,  David M. Engelthaler,  David M. Wagner, Paul Keim

"NASP: an accurate, rapid method for the identification of SNPs in WGS datasets that supports flexible input and output formats". Published Ahead of Print: 21 June, 2016 Microbial Genomics doi: 10.1099/mgen.0.000074 
(http://mgen.microbiologyresearch.org/content/journal/mgen/10.1099/mgen.0.000074)


CONTACT:
--------

| TGen North
| 3051 W Shamrell Blvd Ste 106
| Flagstaff, AZ 86001-9435

| Darrin Lemmer
| dlemmer@tgen.org
| +1-928-226-6374

Owner

  • Name: Translational Genomics Research Institute - Division of Pathogen Genomics
  • Login: TGenNorth
  • Kind: organization
  • Location: Flagstaff, AZ

GitHub Events

Total
  • Push event: 1
  • Create event: 1
Last Year
  • Push event: 1
  • Create event: 1

Committers

Last synced: over 2 years ago

All Time
  • Total Commits: 469
  • Total Committers: 13
  • Avg Commits per committer: 36.077
  • Development Distribution Score (DDS): 0.52
Past Year
  • Commits: 3
  • Committers: 1
  • Avg Commits per committer: 3.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Jason Travis j****s@t****g 225
DarwinW13 d****r@t****g 85
David E Smith d****h@t****g 65
Jason Sahl j****l@g****m 37
David E Smith t****g 28
maziz2 m****2@t****g 6
Jason Travis J****s@n****u 6
Jason Sahl j****l@t****g 4
David Smith d****h@t****g 4
David E Smith d****h@g****m 3
Juan MONROY-NIETO 1****o 3
Darrin Lemmer d****n@l****t 2
Jason Travis j****s@i****g 1
Committer Domains (Top 20 + Academic)
tgen.org: 5 it3019.ad.tgen.org: 1 lemmerfamily.net: 1 tnorth-login.tgen.org: 1 nau.edu: 1

Issues and Pull Requests

Last synced: about 1 year ago

All Time
  • Total issues: 21
  • Total pull requests: 3
  • Average time to close issues: over 1 year
  • Average time to close pull requests: 2 days
  • Total issue authors: 16
  • Total pull request authors: 2
  • Average comments per issue: 1.95
  • Average comments per pull request: 0.33
  • Merged pull requests: 2
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 0
  • Pull request authors: 0
  • Average comments per issue: 0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • malihaaziz (3)
  • mkleinecke (2)
  • dpchris (2)
  • sariya (2)
  • KasperThystrup (1)
  • AmayaCLagos (1)
  • mdrishti (1)
  • siahahmed (1)
  • zhaoxvwahaha (1)
  • ocarabali (1)
  • r0sies (1)
  • OrsonMM (1)
  • chrisgulvik (1)
  • luciahenrici (1)
  • AdrianAllen1977 (1)
Pull Request Authors
  • DarwinW13 (2)
  • jbaksta (1)
Top Labels
Issue Labels
wontfix (1)
Pull Request Labels

Packages

  • Total packages: 4
  • Total downloads:
    • pypi 23 last-month
  • Total dependent packages: 0
    (may contain duplicates)
  • Total dependent repositories: 2
    (may contain duplicates)
  • Total versions: 26
  • Total maintainers: 1
proxy.golang.org: github.com/tgennorth/nasp
  • Versions: 7
  • Dependent Packages: 0
  • Dependent Repositories: 0
Rankings
Forks count: 3.7%
Stargazers count: 4.6%
Average: 6.2%
Dependent packages count: 7.0%
Dependent repos count: 9.3%
Last synced: 11 months ago
proxy.golang.org: github.com/TGenNorth/NASP
  • Versions: 7
  • Dependent Packages: 0
  • Dependent Repositories: 0
Rankings
Dependent packages count: 7.0%
Average: 8.2%
Dependent repos count: 9.3%
Last synced: 12 months ago
proxy.golang.org: github.com/TGenNorth/nasp
  • Versions: 7
  • Dependent Packages: 0
  • Dependent Repositories: 0
Rankings
Dependent packages count: 7.0%
Average: 8.2%
Dependent repos count: 9.3%
Last synced: 11 months ago
pypi.org: nasp

Northern Arizona SNP Pipeline

  • Versions: 5
  • Dependent Packages: 0
  • Dependent Repositories: 2
  • Downloads: 23 Last month
Rankings
Dependent packages count: 10.0%
Forks count: 10.9%
Dependent repos count: 11.6%
Stargazers count: 13.9%
Average: 19.0%
Downloads: 48.5%
Maintainers (1)
Jason.Travis
Last synced: 11 months ago

Dependencies

nasp/nasptool/go.mod go
  • github.com/pkg/errors v0.8.1
nasp/nasptool/go.sum go
  • github.com/pkg/errors v0.8.1