Comparative assemblies: Difference between revisions
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== AMOScmp pipeline == | == AMOScmp pipeline == | ||
Short reads(Solexa) | |||
=== Modified parameters === | === 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: | * 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 | -D MINMATCH=20 -D MINCLUSTER=20 | ||
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* Use '''make-consensus''' -x option ??? | * Use '''make-consensus''' -x option ??? | ||
* Use '''promer''' instead of '''nucmer''': alignement/cluster sizes of 6/11 (in AA) | * 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 | |||
=== Multiple references === | === Multiple references === | ||
Revision as of 17:47, 26 February 2008
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