Usage

CRAM is invoked via the command-line.

Setting up an experiment

CRAM is a collection of tools used for creating metagenomics pipelines. Pipelines are defined in scripts that follow this pattern:

from metacram import *

# do metagenome things using metacram

There are two pipelines included with this packages: Illumina and Roche 454 for analyzing metagenomes produced by their respective sequencing technologies. To define your own pipeline, see the docs.

One can create a project for analyzing an Illumina metagenome like this:

metacram illumina ~/baby_drool_microbiome/

A CRAM Project contains the pipeline script and a directory structure that contains the output of the various analyses that looks like this:

# Main Directory
cram/

# Input
cram/data               # Raw Reads (left.qseq and right.qseq for illumina)
cram/db                 # Databases

# Output
cram/out/               
├── trimmed             # Trimmed reads
├── contigs_31          # contigs at K = 31
├── contigs_51          #                51
├── contigs_71          #                71
├── contigs_final       # Previous assemblies joined, assembled w/ K = 51
├── orfs                # ORF predictions
├── anno                # PHMMER protein annotations
├── refs                # Reference assemblies
└── tables              # Output tables

CRAM checks for output files and will skip any steps that have already been completed. If you want to re-do a step, delete the appropriate output directory or file(s).

This will clone a fresh copy of CRAM into your experiment directory. However, the db/ and bin/ directories will be empty. Instead of copying these directories (which can be large), use symbolic links.

This will save space and create consistency between experiments

Merging Output

Output tables can be merged into Functional and Taxonomic Abundancy Matrices. These matrices can be merged allowing for standardization, normalization, visualization and analysis of results.

There are scripts located in the tools/ directory to help achieve this.