Comparative assemblies

AMOScmp pipeline

Short reads(Solexa)

Modified parameters

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

Read trimming

 * Quality trimming: to stringent

 * Align to reference using nucmer (small -c -l); trim reads to alignment coordinates
 * Identify 0 cvg regions; don't trim reads adjacent to these regions
 * Update read clr's; run AMOScmp