Comparative assemblies

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AMOScmp pipeline

Modified parameters

 * Smaller alignement/cluster sizes : default are 20/65 ; drop to 16/16 ; as low as 14/14; 12/12 gives too many  spurious alignments:
   -D MINCLUSTER=20 
 * Drop min ovl from 10 to 5: 
   -D MINOVL=5 
 * Drop majority from 70 to 50: 
   -D MAJORITY=50 
 * Drop wiggle from 15 to 2
   -D ALIGNWIGGLE=2
 * Use promer instead of nucmer: alignement/cluster sizes of 6/11 (in AA)

Multiple references