# a small example of a parameter file for MIRA
#
# basically, it does the same thing as the 'demo1' example
#  EXCEPT it does not search for repetitive sequences!
#  That is, there will be misassembled repeats present in the
#  contigs (you will spot them easily)
#  

#
# name all the input and output files starting with 'demo2'
# setting this should be done as very first option
#

--project=demo3


# we want an assembly from scratch (denovo), it's genomic data,
#  "normal" assembly accuracy and it's sanger data

-job=denovo,genome,normal,sanger 

#
# by todays standard the data is low quality
#

-lowqualitydata 


# switch to settings for SANGER data

SANGER_SETTINGS

#
# Tell mira to load a 'file of filenames' that contains
#  filenames of sequences in EXP format

-LOADREADS:
ft=fofnexp

# do not load XML ancillary data (we don't have it, all we need is
#  in the EXP files anyway

mxti=no


# switch to settings for common data

COMMON_SETTINGS

# we need to load qualities from the SCF files (that's the only thing
#  not present in these EXP files)

eq=scf  


#
# ... but our input file is not in this directory (and has
#  has another name than the expected standard)
#

-FILENAME:
fofnexpin=../data/exp_set1/fofn

#
# The experiment and SCF files are in separate directories, too
#

-DIRECTORY:
exp=../data/exp_set1
scf=../data/scf

