assembbly module present -- addedd SOAPdenovo
assembly.py added
added script om utils to quality and hard trim reads
QC delivery report finished
added merged_overlapping_read.py
ABySS, SOAPdenovo, SPADES fully supported
not tracking QC_report.py
script to automatically run de novo assemblies on high number of single libraries
changed logic in ceating DATA directory, need to double check if QCcontrol works
fixed typo in abyss assembly routine
added amanita config file and fixed problem with argument passing in SOAPdenovo
Major changes to the pipeline
added new tools to pipeline
fix problem with running abyss kmer
added config for uppmax
working on amanita
remover QCcontrol.pyc from working tree
bug fixes for picea, succesfully rin evalaution
bug fixes, now pdf is not produced but must be exported to local computer and compiled/edited
adding ALLPATHS3 as assembler, still to complitely test