This folder contain an example show how to run IMR/DENOM for assembly.
Please install IMR/DENOM first, download this example and decompress it.


Case 1: Running IMR/DENOM from scratch
#======================
cd example
imrdenom example2.t

Case 2: Running IMR/DENOM with denovo assembled contigs available
## running IMR
cd example
imr easyrun example2.t
##running DENOM
##It can be run without IMR being finished 
denom easyrun ./testdata/tair10_um.fa ./testdata/bur_0.contigs.50 bur.denom.bam bur0.denom.sdi
##running MCMERGE
##Please download simulation file (sim_tair10.bam) from http://mus.well.ox.ac.uk/imrdenom/simbam/
mcmerge easyrun -p 6 ./testdata/tair10_um.fa ./bur_example2/pro/result_imr.sdi bur0.denom.sdi ./bur_example2/A/bur_example2_A.bam bur.denom.bam sim_tair10.bam      



Note: The pair end data used in this example is produced in WTCHG financed by Richard Mott. The single end data is from EBI archive and produced by Detlef Weigel's group. These are all the data used when reassembling the bur-0 and you should be able to get a close result as we published in paper "Multiple reference genomes and transcriptomes for Arabidopsis thaliana Nature 2011".