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


 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, VCF, and SNP-matrix (TSV) 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 <reference.fasta> [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 --config <path_to_config.xml>


 INSTALLATION:
---------------
See the included "INSTALL" document.


 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 included
"INSTALL" document.


 LICENSE:
----------
Copyright (c) The Translational Genomics Research Institute
See the included "LICENSE" document.


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

  David Smith
  dsmith@tgen.org
  +1-928-226-6381

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