RNAseq-Pi - A general, flexible, modular and scalable RNAseq Pipeline.

Copyright (C) 2011 Juan Caballero [Institute for Systems Biology]

DESCRIPTION

RNAseq-Pi is a collection of programs (modules) to run transcriptomic analysis 
in RNAseq samples.

The modules can be classified as:
    a) Composition filters
    b) Homology filters
    c) Sequence mapping
    d) Special operations
    
A typical pipeline can be defined:

+------------+
| FASTA /    |      +-----------------------------+
| FASTQ file | ---> |      Preprocessing          |
+------------+      +-----------------------------+
                                |
								|
                               \|/ 
                    +-----------------------------+
                    |     Low quality filter      | ---> Bad reads 
                    +-----------------------------+
                                |
								|
                               \|/
                    +-----------------------------+
                    |       Vector filter         | ---> Bad reads
                    +-----------------------------+
                                |
								|
                               \|/
                    +-----------------------------+
                    |     Low complexity filter   | ---> Bad reads
                    +-----------------------------+
                                |
								|
                               \|/
                    +-----------------------------+
                    |     Ribosomal + MT filter   | ---> Uninformative reads
                    +-----------------------------+
                                |
								|
                               \|/
                    +-----------------------------+
                    |    Repeat consensus filter  | ---> Uninformative reads
                    +-----------------------------+
                                |
								|
                               \|/
                    +-----------------------------+
                    |       Spike-ins filter      | ---> QC/Normalization reads
                    +-----------------------------+
                                |
								|
                               \|/
                    +-----------------------------+
                    |   Mapping                   |
                    |       Regular               |
                    |           Transcripts       |
                    |           Genome            | ---> Informative reads 
                    |           Predicted splices |          |
                    |       MapSplice             |          +---> CUFFLINKS
                    +-----------------------------+
                                |
								|
                               \|/
                    +-----------------------------+
                    |Other genome conservation    |
                    |Assembly                     |
                    |Contamination verification   | ---> ? reads
                    |???                          |
                    +-----------------------------+
                    
As mentioned above, many steps can be ommited or in different order (modular) 
or can use diferent aligners like bowtie, bwa or blat (flexibility).

CITATION

Caballero J ... 

LICENSE

All the code is under the GPLv3 licence, see LICENSE file for details.