Reference genomes for yeast and E. coli:
yeast_S288C_ref.fa
ecoli_K12_MG1665_ref.fa

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Six datasets:
ecoli_R7_2D.fa
ecoli_R73_2D.fa
ecoli_UCSC_phase1b_2D.fa
ecoli_R9_1D.fa
ecoli_R9_2D.fa
yeast_2D.fa

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The six zip files are profiles of these four datasets. After downloading and unzipping, put the profiles in the same directory for simulation. Run simulator.py directly and in -c option, provide the prefix of the profiles.