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)