Comparative assemblies: Difference between revisions
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=== Modified parameters === | === 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: | * 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 MINCLUSTER=20 | -D MINMATCH=20 -D MINCLUSTER=20 | ||
* Drop min ovl from 10 to 5: | * Drop '''casm-layout''' min ovl from 10 to 5: | ||
-D MINOVL=5 | -D MINOVL=5 | ||
* Drop majority from 70 to 50: | * Drop '''casm-layout''' majority from 70 to 50: | ||
-D MAJORITY=50 | -D MAJORITY=50 | ||
* Drop wiggle from 15 to 2 | * Drop '''make-consensus''' alignment wiggle from 15 to 2 | ||
-D ALIGNWIGGLE=2 | -D ALIGNWIGGLE=2 | ||
* Use promer instead of nucmer: alignement/cluster sizes of 6/11 (in AA) | * Use '''make-consensus''' -x option ??? | ||
* Use '''promer''' instead of '''nucmer''': alignement/cluster sizes of 6/11 (in AA) | |||
=== Multiple references === | === Multiple references === | ||
Revision as of 17:42, 26 February 2008
AMOScmp pipeline
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)