Assembly merge - Revision history

Dpuiu at 01:21, 2 September 2010

2010-09-02T01:21:33Z

← Older revision		Revision as of 01:21, 2 September 2010
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	See [[Dpuiu_CA\|CA]]		See [[Dpuiu_CA\|CA]]

			=== Abyss ===
			* [http://www.bcgsc.ca/platform/bioinfo/software/abyss Abyss]

	=== Atlas ===		=== Atlas ===

2010-01-22T21:45:41Z

maq

← Older revision		Revision as of 21:45, 22 January 2010
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	=== maq ===		=== maq ===

			* Version: 0.6.6
			* [http://maq.sourceforge.net/ Web site]
	* At high %identity (close to 100%) maq outperforms AMOScmp-shortReads-alignmentTrimmed		* At high %identity (close to 100%) maq outperforms AMOScmp-shortReads-alignmentTrimmed
	* At lower % identity (<97%) AMOScmp-shortReads-alignmentTrimmed outperforms maq		* At lower % identity (<97%) AMOScmp-shortReads-alignmentTrimmed outperforms maq

2010-01-22T21:44:11Z

AMOScmp

← Older revision		Revision as of 21:44, 22 January 2010
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	=== AMOScmp ===		=== AMOScmp ===

			* [http://sourceforge.net/apps/mediawiki/amos/index.php?title=AMOScmp Web site]
	* one should increase the make-consensus error rate if ref and qry are not that similar		* one should increase the make-consensus error rate if ref and qry are not that similar
	* all reads from layout are included in consensus		* all reads from layout are included in consensus

2010-01-13T19:35:01Z

Velvet

← Older revision		Revision as of 19:35, 13 January 2010
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	Example (unmated reads):		Example (unmated reads):
	$ velveth . ovl prefix.seq # ovl should be an odd integer like 21, 23		$ velveth . -[short\|shortPaired\|long\|longPaired] ovl prefix.seq # ovl should be an odd integer like 21, 23
	$ velvetg . -read_trkg yes		$ velvetg . -read_trkg yes

2010-01-13T18:58:57Z

SOAPdenovo

← Older revision		Revision as of 18:58, 13 January 2010
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	* Location (turkey)		* Location (turkey)
	/scratch1/dpuiu/SOAPdenovo/turkey/		/scratch1/dpuiu/SOAPdenovo/turkey/

			=== Mira ===
			* http://www.chevreux.org/projects_mira.html
			* Sanger, 454 and Solexa /Illumina
			* supposed to be "very" slow

	== Others ==		== Others ==

2010-01-11T18:34:58Z

newbler (454)

← Older revision		Revision as of 18:34, 11 January 2010
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	=== newbler (454) ===		=== newbler (454) ===

			* Command:
			/fs/sz-user-supported/Linux-x86_64/packages/rig/bin/runAssembly -o dir prefix.sff

	=== minimus ===		=== minimus ===

2009-12-15T19:22:41Z

SOAPdenovo

← Older revision		Revision as of 19:22, 15 December 2009
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	/nfshomes/dpuiu/szdevel/SOAPdenovo_Release1.03/SOAPdenovo all -s SOAPdenovo.config -o out		/nfshomes/dpuiu/szdevel/SOAPdenovo_Release1.03/SOAPdenovo all -s SOAPdenovo.config -o out

	* Example turkey: ~~pairee~~		* Example turkey: paires

	elem min q1 q2 q3 max mean n50 sum		elem min q1 q2 q3 max mean n50 sum
	reads 88357456 76 76 76 76 76 76 76 6715166656 # 44178728 mates; 2.39X cvg		reads 88357456 76 76 76 76 76 76 76 6715166656 # 44178728 mates; 2.39X cvg
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	scf 982536 100 258 517 1080 16376 839 1411 825003003		scf 982536 100 258 517 1080 16376 839 1411 825003003

			85505015 out.readOnContig
	* Location (turkey)		* Location (turkey)
	/scratch1/dpuiu/SOAPdenovo/turkey/		/scratch1/dpuiu/SOAPdenovo/turkey/

2009-12-15T17:24:39Z

SOAPdenovo

← Older revision		Revision as of 17:24, 15 December 2009
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	* http://soap.genomics.org.cn/soapdenovo.html		* http://soap.genomics.org.cn/soapdenovo.html
	* Release 1.03 , 06-09-2009		* Release 1.03 , 06-09-2009
	* Example config ~~(single reads)~~		* Example config
	~~$ cat SOAPdenovo.config~~		[LIB] # single reads
	~~#max_rd_len=35~~
	[LIB]
	f=in.fa		f=in.fa
			[LIB] # paired reads
	* Example config (paired reads)		avg_ins=180
	~~$ cat SOAPdenovo~~.~~config~~		f1=fwd.seq
	~~max_rd_len~~=76		f2=rev.seq
	[LIB]		[LIB] # paired reads
	avg_ins=180		avg_ins=180
	f1=~~/scratch1/dpuiu/SOAPdenovo/turkey/Illumina.fwd.seq~~		p=in.seq
	~~f2=/scratch1/dpuiu/SOAPdenovo/turkey/Illumina.rev~~.seq

	* Example run:		* Example run:
	$ cat SOAPdenovo.sh		$ cat SOAPdenovo.sh
	/nfshomes/dpuiu/szdevel/SOAPdenovo_Release1.03/SOAPdenovo all -s SOAPdenovo.config -o out		/nfshomes/dpuiu/szdevel/SOAPdenovo_Release1.03/SOAPdenovo all -s SOAPdenovo.config -o out

			* Example turkey: pairee

			elem min q1 q2 q3 max mean n50 sum
			reads 88357456 76 76 76 76 76 76 76 6715166656 # 44178728 mates; 2.39X cvg
			ctg 4664917 24 25 36 156 13863 198 761 926637298
			scf 982536 100 258 517 1080 16376 839 1411 825003003

	* Location (turkey)		* Location (turkey)

2009-12-14T20:26:25Z

SOAPdenovo

← Older revision		Revision as of 20:26, 14 December 2009
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	* http://soap.genomics.org.cn/soapdenovo.html		* http://soap.genomics.org.cn/soapdenovo.html
	* Release 1.03 , 06-09-2009		* Release 1.03 , 06-09-2009
	* EX config (single reads)		* Example config (single reads)
	$ cat SOAPdenovo.config		$ cat SOAPdenovo.config
	#max_rd_len=35		#max_rd_len=35

2009-12-14T20:26:12Z

SOAPdenovo

← Older revision		Revision as of 20:26, 14 December 2009
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	* http://soap.genomics.org.cn/soapdenovo.html		* http://soap.genomics.org.cn/soapdenovo.html
	* Release 1.03 , 06-09-2009		* Release 1.03 , 06-09-2009
	* ~~Example~~		* EX config (single reads)
	$ cat SOAPdenovo.config		$ cat SOAPdenovo.config
	#max_rd_len=35		#max_rd_len=35
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	f=in.fa		f=in.fa

			* Example config (paired reads)
			$ cat SOAPdenovo.config
			max_rd_len=76
			[LIB]
			avg_ins=180
			f1=/scratch1/dpuiu/SOAPdenovo/turkey/Illumina.fwd.seq
			f2=/scratch1/dpuiu/SOAPdenovo/turkey/Illumina.rev.seq

			* Example run:
	$ cat SOAPdenovo.sh		$ cat SOAPdenovo.sh
	~~!#/bin/sh~~
	/nfshomes/dpuiu/szdevel/SOAPdenovo_Release1.03/SOAPdenovo all -s SOAPdenovo.config -o out		/nfshomes/dpuiu/szdevel/SOAPdenovo_Release1.03/SOAPdenovo all -s SOAPdenovo.config -o out

	* ~~Example~~ (turkey)		* Location (turkey)
	/scratch1/dpuiu/SOAPdenovo/turkey		/scratch1/dpuiu/SOAPdenovo/turkey/

	== Others ==		== Others ==