cgat.py - Computational Genomics Analysis Tools
===============================================

:Tags: Genomics

To use a specific tool, type::

    cgat <tool> [tool options] [tool arguments]

Tools are grouped by keywords. For this message and a list of
available keywords type::

    cgat --help

For a list of tools matching a certain keyword, type::

   cgat --help <keyword>

or::

   cgat --help all

for a list of all available tools.

To get help for a specific tool, type::

    cgat <tool> --help

cgat tools are grouped by keywords. The following keywords
are defined:

Genomics              FASTQ                 Annotation           
NGS                   GenomeAlignment       MultipleAlignments   
Geneset               PSL                   Counting             
BAM                   CHAIN                 Fasta                
Manipulation          Summary               Variants             
Intervals             Comparison            Protein              
BED                   FASTA                 WIGGLE               
GFF                   Sequences             BIGWIG               
Conversion            Genesets              BEDGRAPH             
Python                GTF