A Shotgun Metagenome Annotation Pipeline
Version: v1.1
Shotmap is a software workflow that functionally annotates and compares shotgun metagenomes. Specifically, it will:
- Compared unassembled or assembled metagenomic sequences to a protein family database
- Calculate metagenome functional abundance and diversity
- Compare metagenomes using a variety of statistical and ecological tools
- 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/build_shotmap_searchdb.pl -r=</directory/path/to/reference/database> -d=</directory/path/to/search/database>
And then execute ShotMAP:
perl $SHOTMAP_LOCAL/scripts/shotmap.pl -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/compare_shotmap_results.pl -i=</directory/path/to/result/database/> -m=</path/to/optional/metadata/file> -o=</directory/path/to/new/result/directory/>
- Workflow Synopsis
- Overview on How to Run ShotMAP
- Dependencies
- Installation Guide
- Building a ShotMAP Search Database
- Metadata Files
- Workflow Output
- Script Documentation
- Advanced Documentation
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/run_tests.pl
- change in rapsearch options to reduce disc footpring