Post date: Nov 03, 2014 10:24:46 PM
The results using a minimum cluster size of 1000 bp were very encouraging. This cleans up the alignment with most points now falling on or near the diagonal. Next I am trying the same conditions for L. warner vs. each of the other genomes, e.g.,
/home/A01963476/Source/MUMmer3.23/nucmer --mum -c 1000 -l 15 -g 1000 --prefix=mumLanna_Lwarner1k Lanna/DATA/RUN/ASSEMBLIES/assem18sept14/final.assembly.fasta Lwarner/DATA/RUN/ASSEMBLIES/assem12oct14/final.assembly.fasta
/home/A01963476/Source/MUMmer3.23/nucmer --mum -c 1000 -l 15 -g 1000 --prefix=mumLidas_Lwarner1k Lidas/DATA/RUN/ASSEMBLIES/assem9oct14/final.assembly.fasta Lwarner/DATA/RUN/ASSEMBLIES/assem12oct14/final.assembly.fasta
/home/A01963476/Source/MUMmer3.23/nucmer --mum -c 1000 -l 15 -g 1000 --prefix=mumLmelissa_Lwarner1k Lmelissa/DATA/RUN/ASSEMBLIES/assem22sept14/final.assembly.fasta Lwarner/DATA/RUN/ASSEMBLIES/assem12oct14/final.assembly.fasta
/home/A01963476/Source/MUMmer3.23/nucmer --mum -c 1000 -l 15 -g 1000 --prefix=mumLmel1_Lwarner1k ../melissa_genome/final.assembly.fasta Lwarner/DATA/RUN/ASSEMBLIES/assem12oct14/final.assembly.fasta