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
Name | Last commit | Last update |
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ftp | ||
pipeline | ||
ui | ||
.gitignore | ||
README | ||
behavior.py | ||
git | ||
mktree.sh | ||
rsync | ||
run | ||
showdiff.sh |