Comparative assemblies - Revision history

Dpuiu: /* Modified parameters */

2008-02-27T13:51:44Z

Modified parameters

← Older revision		Revision as of 13:51, 27 February 2008
Line 5:		Line 5:
	=== Modified parameters ===		=== Modified parameters ===

			Modified AMOScmp pipeline: ~dpuiu/bin/AMOScmp

	Alignment:		Alignment:
	* Lower '''nucmer''' alignement/cluster sizes : default are 20/65 ; drop to 16/16 (Solexa_read_len/2)		* Lower '''nucmer''' alignement/cluster sizes : default are 20/65 ; drop to 16/16 (Solexa_read_len/2)

Dpuiu at 20:36, 26 February 2008

2008-02-26T20:36:24Z

← Older revision		Revision as of 20:36, 26 February 2008
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	=== Read trimming ===		=== Read trimming ===

	* Quality trimming: to stringent		* Quality trimming: too stringent

	* Align to reference using nucmer (small -c <n> -l <n>); trim reads to alignment coordinates		* Align to reference using nucmer (small -c <n> -l <n>); trim reads to alignment coordinates

Dpuiu: /* Modified parameters */

2008-02-26T20:30:14Z

Modified parameters

← Older revision		Revision as of 20:30, 26 February 2008
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	* Drop '''casm-layout''' majority from 70 to 50:		* Drop '''casm-layout''' majority from 70 to 50:
	-D MAJORITY=50		-D MAJORITY=50

	Consensus:		Consensus:
	* Drop '''make-consensus''' alignment wiggle from 15 to 2		* Drop '''make-consensus''' alignment wiggle from 15 to 2

Dpuiu: /* Modified parameters */

2008-02-26T20:30:06Z

Modified parameters

← Older revision		Revision as of 20:30, 26 February 2008
Line 5:		Line 5:
	=== Modified parameters ===		=== Modified parameters ===

	* ~~Smaller~~ '''nucmer''' alignement/cluster sizes : default are 20/65 ; drop to 16/16 (Solexa_read_len/2)		Alignment:
			* Lower '''nucmer''' alignement/cluster sizes : default are 20/65 ; drop to 16/16 (Solexa_read_len/2)
	Can go as low as 14/14; 12/12 gives too many spurious alignments:		Can go as low as 14/14; 12/12 gives too many spurious alignments:
	-D MINMATCH=20 -D MINCLUSTER=20		-D MINMATCH=20 -D MINCLUSTER=20
			* Run nucmer multiple times:
			all reads: given alignement/cluster size
			unaligned reads: smaller alignement/cluster size
			unaligned reads: smaller alignement/cluster size
			...
			* Use '''promer''' instead of '''nucmer''': alignement/cluster sizes of 6/11 (in AA)

			Layout:
	* Drop '''casm-layout''' min ovl from 10 to 5:		* Drop '''casm-layout''' min ovl from 10 to 5:
	-D MINOVL=5		-D MINOVL=5
	* Drop '''casm-layout''' majority from 70 to 50:		* Drop '''casm-layout''' majority from 70 to 50:
	-D MAJORITY=50		-D MAJORITY=50

			Consensus:
	* Drop '''make-consensus''' alignment wiggle from 15 to 2		* Drop '''make-consensus''' alignment wiggle from 15 to 2
	-D ALIGNWIGGLE=2		-D ALIGNWIGGLE=2
	* Use '''make-consensus''' -x option ???		* Use '''make-consensus''' -x option ???
	* Use '''promer''' instead of '''nucmer''': alignement/cluster sizes of 6/11 (in AA)

	=== Read trimming ===		=== Read trimming ===

Dpuiu at 20:23, 26 February 2008

2008-02-26T20:23:32Z

← Older revision		Revision as of 20:23, 26 February 2008
Line 42:		Line 42:

	Example:		Example:
	$ ~~~dpuiu/bin/~~fastaMerge.pl -min 5 -max 30 -id 0.8 $(PREFIX).fasta -debug 1 > $(PREFIX).merge.fasta		$ fastaMerge.pl -min 5 -max 30 -id 0.8 $(PREFIX).fasta -debug 1 > $(PREFIX).merge.fasta

	ctg1_id ctg2_id ovl_len ovl_id		ctg1_id ctg2_id ovl_len ovl_id

Dpuiu at 20:22, 26 February 2008

2008-02-26T20:22:45Z

← Older revision		Revision as of 20:22, 26 February 2008
Line 5:		Line 5:
	=== 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 (Solexa_read_len/2)
			Can go as low as 14/14; 12/12 gives too many spurious alignments:
	-D MINMATCH=20 -D MINCLUSTER=20		-D MINMATCH=20 -D MINCLUSTER=20
	* Drop '''casm-layout''' min ovl from 10 to 5:		* Drop '''casm-layout''' min ovl from 10 to 5:
Line 20:		Line 21:
	* Quality trimming: to stringent		* Quality trimming: to stringent

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

			Example:
			$ show-coords -c -l -o -r -H $(PREFIX).delta \| $(SCRIPTDIR)/getNucmerCoverage.pl -M 0 > $(PREFIX).0cvg
			$ delta2clr.pl -zero_cvg $(PREFIX).0cvg -read_len $(READLEN) < $(PREFIX).delta > $(PREFIX).clr
			$ awk '{print $1}' $(PREFIX).clr > $(PREFIX).seqs
			$ updateClrRanges -i $(PREFIX).bnk $(PREFIX).clr
			$ dumpreads -I $(PREFIX).seqs $(BANK) > $(PREFIX).seq

	=== Contig merging ===		=== Contig merging ===
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	* fastaMerge.pl		* fastaMerge.pl
	Input: multiFasta file; contigs must be ordered and oriented; only checks adjacent contig ends		Input: multiFasta file; contigs must be ordered and oriented; only checks adjacent contig ends
	Example: ~dpuiu/bin/fastaMerge.pl -min 5 -max 30 -id 0.8 ~~file~~.fasta -debug 1 > ~~file~~.merge.fasta
			Example:
			$ ~dpuiu/bin/fastaMerge.pl -min 5 -max 30 -id 0.8 $(PREFIX).fasta -debug 1 > $(PREFIX).merge.fasta

	ctg1_id ctg2_id ovl_len ovl_id		ctg1_id ctg2_id ovl_len ovl_id
	20 21 10 1		20 21 10 1

Dpuiu: /* Multiple references */

2008-02-26T20:18:16Z

Multiple references

← Older revision		Revision as of 20:18, 26 February 2008
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	=== Multiple references ===		=== Multiple references ===

			* Find most similar genome : most number or reads it aligns to it

Dpuiu: /* Contig merging */

2008-02-26T20:17:27Z

Contig merging

← Older revision		Revision as of 20:17, 26 February 2008
Line 27:		Line 27:

	* Identify adjacent contig end overlaps		* Identify adjacent contig end overlaps
			* Overlaps might be too short to be identified by alignment programs
	* Programs that do alignment & sequence merging:		* Programs that do alignment & sequence merging:
	* EMBOSS merger: does not handle long sequences		* EMBOSS merger: does not handle long sequences
Line 37:		Line 38:
	36 37 9 0.88		36 37 9 0.88
	...		...
	2008_0109_AMOSCmp-PA14-relaxed-17-nucmer-redo2 assembly: # contigs 2053 -> 1927		2008_0109_AMOSCmp-PA14-relaxed-17-nucmer-redo2 assembly: # contigs 2053 -> 1927

	=== Multiple references ===		=== Multiple references ===

Dpuiu at 20:12, 26 February 2008

2008-02-26T20:12:42Z

← Older revision		Revision as of 20:12, 26 February 2008
Line 24:		Line 24:
	* Update read clr's; run AMOScmp		* Update read clr's; run AMOScmp

			=== Contig merging ===

			* Identify adjacent contig end overlaps
			* Programs that do alignment & sequence merging:
			* EMBOSS merger: does not handle long sequences
			* fastaMerge.pl
			Input: multiFasta file; contigs must be ordered and oriented; only checks adjacent contig ends
			Example: ~dpuiu/bin/fastaMerge.pl -min 5 -max 30 -id 0.8 file.fasta -debug 1 > file.merge.fasta
			ctg1_id ctg2_id ovl_len ovl_id
			20 21 10 1
			34 35 18 1
			36 37 9 0.88
			...
			2008_0109_AMOSCmp-PA14-relaxed-17-nucmer-redo2 assembly: # contigs 2053 -> 1927

	=== Multiple references ===		=== Multiple references ===

Dpuiu at 17:47, 26 February 2008

2008-02-26T17:47:29Z

← Older revision		Revision as of 17:47, 26 February 2008
Line 1:		Line 1:
	== 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
Line 12:		Line 15:
	* 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 ===