2009-07-20

# Readme for GenomeMapper's multiple genomes test data

################## gmindex ############################

# These three files feature genome variations of three
# different A. thaliana genomes:

Variations.Bur-0.txt
Variations.Tsu-1.txt
Variations.Est-1.txt

# Together with the reference sequence in the file

TAIR8.masked.fa

# they have been used to generate a GenomeMapper index.
# For the graph version such an index constits of 2 
# files:

TAIR8.masked.Bur-0.Tsu-1.Est-1.idx
TAIR8.masked.Bur-0.Tsu-1.Est-1.mta

# In order to re-generate your own version of these two 
# files above, start gmindex by typing:
# (this might take more than 30 min)

gmindex -i TAIR8.masked.fa -x TAIR8.masked.idx -t TAIR8.masked.mta -s 12 -v -d Variations.Bur-0.txt,Variations.Tsu-1.txt,Variations.Est-1.txt

# Though they will have a different naming

TAIR8.masked.idx
TAIR8.masked.mta

# their content is the same is the two index files in
# test data provided. 


################## genomemapper #######################

# To map the test reads against

genomemapper -i TAIR8.masked.fa -x TAIR8.masked.Bur-0.Tsu-1.Est-1.idx -t TAIR8.masked.Bur-0.Tsu-1.Est-1.mta -q Est-1.reads.fa -o alignments.txt


