There are two folders each containing its own README file:
    FTP
        Folder containing scripts to create the FTP structure with decompression,
        quality check and checksum.

    PIPELINE
        Folder containing scripts to trim, clean and correct raw data, as well as
        to expose the final files to assembly.

ftp/mkfolders.py
    Integral part of the project. created the folder structure for the project
    and a list of all the files in the expected places as well as their project
    informatiom such as library, species, etc. as described in setup.py.
    Saves the information in PROJECT_ROOT/project_description.csv

ftp/folderStruct.py
    This script defines the folder structure of the project and some variables of
    the data such as genome size, etc.

behavior.py
    This script contains all the program's variables.

setup.json
    Dump of folderStruct.py and behavior.py so that it can be read in parallel
    and independently as well as to have a saved description of all parameters
    used.

 
Last updated: Thu Sep 13 12:33:27 CEST 2012
Variables   :
    Qborder: 30 - calculates Q30
    Contamination Cleaning:
        454     : threshold = 85% identity
        illumina: threshold = 95% identity
    Genome Size : 950.000.000 = 950 M bases
    Jellyfish:
        both-strands
        high       : 300 - size of the graphic
        mer-len    : 19 - kmer length
    Quake:
        ratio: 800
    Trim Fastq: (solexaQA Dynamic trim)
        h: 20 - minimum phred quality
        l: 30 - minimum sequence length