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A Shotgun Metagenome Annotation Pipeline

Version: v1.1


Shotmap is a software workflow that functionally annotates and compares shotgun metagenomes. Specifically, it will:

  1. Compared unassembled or assembled metagenomic sequences to a protein family database
  2. Calculate metagenome functional abundance and diversity
  3. Compare metagenomes using a variety of statistical and ecological tools
  4. Identify protein families that differentiate metagenomes using robust statistical tests

Shotmap can be run on a multicore computer or can optionally interface with an SGE-configured computing cluste (i.e., a cloud). Shotmap can also optionally manage the information and data associated with this workflow in a relational database.


The fastest way to get shotmap working on your data is to first build a search database (which only needs to be done one time):

perl $SHOTMAP_LOCAL/scripts/ -r=</directory/path/to/reference/database> -d=</directory/path/to/search/database>

And then execute ShotMAP:

 perl $SHOTMAP_LOCAL/scripts/ -i=</directory/path/to/metagenomes> -d=</directory/path/to/search/database> -o=</directory/path/to/result/database/>

And then compare the results (if more than one sample):

perl $SHOTMAP_LOCAL/scripts/ -i=</directory/path/to/result/database/> -m=</path/to/optional/metadata/file> -o=</directory/path/to/new/result/directory/>

Documentation Table of Contents

  1. Workflow Synopsis
  2. Overview on How to Run ShotMAP
  3. Dependencies
  4. Installation Guide
  5. Building a ShotMAP Search Database
  6. Metadata Files
  7. Workflow Output
  8. Script Documentation
  9. Advanced Documentation

Change Log

v1.1 - 2016.04.26

  • update to indexed database file names
  • changes to shotmap.R to handle variation in R version
  • error handline in shotmap.R for qvalue calculation
  • bug fixes in installer script to work on more general systems
  • addition of scripts/
  • change in rapsearch options to reduce disc footpring