User:Dpuiu - Revision history

Dpuiu: /* Other */

2011-12-27T15:34:40Z

Other

← Older revision		Revision as of 15:34, 27 December 2011
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	* [[Trace_formatting\|Sequencing]]		* [[Trace_formatting\|Sequencing]]
	* [[dpuiu_CA\|CA]] ; [[Assembly_merge\|Assembly]]		* [[dpuiu_CA\|CA]] ; [[Assembly_merge\|Assembly]]
	* [[dpuiu_Assemblathon\|Assemblathon]]
	* [[dpuiu_HTS\|HTS]]
	* [[Comparative_assemblies\|Comparative assemblies]]		* [[Comparative_assemblies\|Comparative assemblies]]
	* [[Metagenoms\|Metagenomics]]		* [[Metagenoms\|Metagenomics]]
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	* [[Data_formats\|Data formats]]		* [[Data_formats\|Data formats]]
	<!--		<!--
			* [[dpuiu_Assemblathon\|Assemblathon]]
			* [[dpuiu_HTS\|HTS]]
	* [[dpuiu_definitions\|Definitions]]		* [[dpuiu_definitions\|Definitions]]
	* [[dpuiu_meeting_notes\|Meeting notes]]		* [[dpuiu_meeting_notes\|Meeting notes]]

2011-12-27T15:33:49Z

Other

← Older revision		Revision as of 15:33, 27 December 2011
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	= Other =		= Other =
	* [[Trace_formatting\|Sequencing]]		* [[Trace_formatting\|Sequencing]]
	~~* [[dpuiu_alignment\|Alignment]] *~~
	* [[dpuiu_CA\|CA]] ; [[Assembly_merge\|Assembly]]		* [[dpuiu_CA\|CA]] ; [[Assembly_merge\|Assembly]]
	* [[dpuiu_Assemblathon\|Assemblathon]]		* [[dpuiu_Assemblathon\|Assemblathon]]

2011-12-27T15:33:03Z

Test data sets

← Older revision		Revision as of 15:33, 27 December 2011
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	* [[dpuiu_JHU\|JHU]]		* [[dpuiu_JHU\|JHU]]
	-->		-->



	~~= Test data sets =~~

	~~'''Sanger (1)'''~~
	* 23,536 reads ; 11,652 mates; 1 lib : 4.5K mean; 7X cvg
	* Location: /fs/szasmg/Bacteria/F_tularensis/TA_FTP/libs/G878A1.frg

	~~'''Sanger (2)'''~~
	* 100,781 reads ; 50,008 mates; 24 libs : 4.5K & 10K means; 16X cvg
	* Location: /fs/szasmg/Bacteria/F_tularensis/TA_FTP/libs/G*frg

	~~'''Solexa unpaired'''~~
	* 2,659,250 36bp reads
	* Location: /fs/szdata/Solexa/Streptococcus_suis/suisp17/strip3.fna

	~~'''Solexa paired (1)'''~~
	* 142,858 35bp reads;
	* assemble into one 99,995 ctg/scaff by velvet
	* Location /nfshomes/dpuiu/szdevel/velvet/data/test_reads.fa

	~~'''Solexa paired (2)'''~~
	* 92,143 35bp reads;
	* assemble into 1 scaff by velvetp.sh (velveth -shortPaired)
	* assemble into 5 contigs by velvet.sh (velveth)
	* Location /nfshomes/dpuiu/szdevel/velvet/data/test_reads.subset.fa

	~~'''Solexa & 454'''~~
	* [http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?study=SRP001087 E coli Whole Genome Sequencing on 454 and Illumina]
	* Location /fs/szattic-asmg4/dpuiu/Ecoli

2011-12-27T15:32:39Z

CBCB software

@@ Line 86: / Line 86: @@
 -->
-= CBCB software =
 = Test data sets =

2011-12-27T15:32:15Z

Other

← Older revision		Revision as of 15:32, 27 December 2011
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	* [[Vector_trimming\|Vector trimming]]		* [[Vector_trimming\|Vector trimming]]
	* [[Data_formats\|Data formats]]		* [[Data_formats\|Data formats]]
			<!--
	* [[dpuiu_definitions\|Definitions]]		* [[dpuiu_definitions\|Definitions]]
	* [[dpuiu_meeting_notes\|Meeting notes]]		* [[dpuiu_meeting_notes\|Meeting notes]]
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	* [[dpuiu_snp\|Snp calling]]		* [[dpuiu_snp\|Snp calling]]
	* [[dpuiu_todo\|ToDo]]		* [[dpuiu_todo\|ToDo]]

	* [[dpuiu_JHU\|JHU]]		* [[dpuiu_JHU\|JHU]]
			-->

	= CBCB software =		= CBCB software =

2011-12-27T15:31:03Z

Projects

← Older revision		Revision as of 15:31, 27 December 2011
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	* [[Yersinia_pestis\|Yersinia pestis]]		* [[Yersinia_pestis\|Yersinia pestis]]

			<!--
	'''Other genomes'''		'''Other genomes'''
	* [[Bumblebee\|Bombus impatiens]]		* [[Bumblebee\|Bombus impatiens]]
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	* [[Xanthomonas_campestris_pv_raphani\|Xanthomonas campestris pv. raphani]] XCR		* [[Xanthomonas_campestris_pv_raphani\|Xanthomonas campestris pv. raphani]] XCR
	* [[Strawberry\|Strawberry]]		* [[Strawberry\|Strawberry]]


	* [[Ecoli_germany\|Ecoli Germany]]		* [[Ecoli_germany\|Ecoli Germany]]
			-->

	= Other =		= Other =

2011-12-27T15:30:18Z

Links

← Older revision		Revision as of 15:30, 27 December 2011
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	* [http://www.sanger.ac.uk/ Sanger]		* [http://www.sanger.ac.uk/ Sanger]
	* [http://www.sanger.ac.uk/Projects/Microbes/ Sanger Microbial Genomes]		* [http://www.sanger.ac.uk/Projects/Microbes/ Sanger Microbial Genomes]
	* [https://wiki.umiacs.umd.edu/cbcb-private/index.php/Main_Page CBCB]
	** NCBI complete genomes: /fs/szdata//ncbi/genomes/Bacteria/ (*.fna)
	** www -> /fs/www-cbcb/htdocs/
	** Personal web site http://www.cbcb.umd.edu/~dpuiu -> /fs/www/users/dpuiu/
	** Personal ftp site ftp://ftp.cbcb.umd.edu/pub/data/dpuiu -> /fs/ftp-cbcb/pub/data/dpuiu/

	* [http://www.thearkdb.org/arkdb/index.jsp ARKDB] genetic maps - cow, chicken ...		* [http://www.thearkdb.org/arkdb/index.jsp ARKDB] genetic maps - cow, chicken ...

2011-12-27T15:29:44Z

Bookmarks

← Older revision		Revision as of 15:29, 27 December 2011
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	Daniela Puiu's page		Daniela Puiu's page

	~~= Bookmarks =~~
	~~[[dpuiu_Perl\|Perl]] ;~~
	~~[[dpuiu_C\|C]] ;~~
	~~[[dpuiu_Linux\|Linux]];~~
	~~[[dpuiu_Windows\|Windows]];~~
	~~[[dpuiu_R\|R]];~~
	~~[http://www.bioperl.org/wiki/HOWTOs BioPerl HOWTOs];~~

	= NCBI =		= NCBI =

2011-12-27T15:29:11Z

Bookmarks

← Older revision		Revision as of 15:29, 27 December 2011
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	[[dpuiu_R\|R]];		[[dpuiu_R\|R]];
	[http://www.bioperl.org/wiki/HOWTOs BioPerl HOWTOs];		[http://www.bioperl.org/wiki/HOWTOs BioPerl HOWTOs];
	~~[https://wiki.umiacs.umd.edu/cbcb-private/index.php/Compute CBCB computers]~~

	= NCBI =		= NCBI =

2011-06-24T18:12:05Z

Other

← Older revision		Revision as of 18:12, 24 June 2011
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	* [[Vector_trimming\|Vector trimming]]		* [[Vector_trimming\|Vector trimming]]
	* [[Data_formats\|Data formats]]		* [[Data_formats\|Data formats]]

	* [[dpuiu_definitions\|Definitions]]		* [[dpuiu_definitions\|Definitions]]
	* [[dpuiu_meeting_notes\|Meeting notes]]		* [[dpuiu_meeting_notes\|Meeting notes]]
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	* [[dpuiu_snp\|Snp calling]]		* [[dpuiu_snp\|Snp calling]]
	* [[dpuiu_todo\|ToDo]]		* [[dpuiu_todo\|ToDo]]

			* [[dpuiu_JHU\|JHU]]

	= CBCB software =		= CBCB software =

← Older revision		Revision as of 15:34, 27 December 2011
Line 66:		Line 66:
	* [[Trace_formatting\|Sequencing]]		* [[Trace_formatting\|Sequencing]]
	* [[dpuiu_CA\|CA]] ; [[Assembly_merge\|Assembly]]		* [[dpuiu_CA\|CA]] ; [[Assembly_merge\|Assembly]]
	* [[dpuiu_Assemblathon\|Assemblathon]]
	* [[dpuiu_HTS\|HTS]]
	* [[Comparative_assemblies\|Comparative assemblies]]		* [[Comparative_assemblies\|Comparative assemblies]]
	* [[Metagenoms\|Metagenomics]]		* [[Metagenoms\|Metagenomics]]
Line 75:		Line 73:
	* [[Data_formats\|Data formats]]		* [[Data_formats\|Data formats]]
	<!--		<!--
			* [[dpuiu_Assemblathon\|Assemblathon]]
			* [[dpuiu_HTS\|HTS]]
	* [[dpuiu_definitions\|Definitions]]		* [[dpuiu_definitions\|Definitions]]
	* [[dpuiu_meeting_notes\|Meeting notes]]		* [[dpuiu_meeting_notes\|Meeting notes]]

← Older revision		Revision as of 15:33, 27 December 2011
Line 65:		Line 65:
	= Other =		= Other =
	* [[Trace_formatting\|Sequencing]]		* [[Trace_formatting\|Sequencing]]
	~~* [[dpuiu_alignment\|Alignment]] *~~
	* [[dpuiu_CA\|CA]] ; [[Assembly_merge\|Assembly]]		* [[dpuiu_CA\|CA]] ; [[Assembly_merge\|Assembly]]
	* [[dpuiu_Assemblathon\|Assemblathon]]		* [[dpuiu_Assemblathon\|Assemblathon]]

← Older revision		Revision as of 15:32, 27 December 2011
Line 75:		Line 75:
	* [[Vector_trimming\|Vector trimming]]		* [[Vector_trimming\|Vector trimming]]
	* [[Data_formats\|Data formats]]		* [[Data_formats\|Data formats]]
			<!--
	* [[dpuiu_definitions\|Definitions]]		* [[dpuiu_definitions\|Definitions]]
	* [[dpuiu_meeting_notes\|Meeting notes]]		* [[dpuiu_meeting_notes\|Meeting notes]]
Line 82:		Line 83:
	* [[dpuiu_snp\|Snp calling]]		* [[dpuiu_snp\|Snp calling]]
	* [[dpuiu_todo\|ToDo]]		* [[dpuiu_todo\|ToDo]]

	* [[dpuiu_JHU\|JHU]]		* [[dpuiu_JHU\|JHU]]
			-->

	= CBCB software =		= CBCB software =

← Older revision		Revision as of 18:12, 24 June 2011
Line 87:		Line 87:
	* [[Vector_trimming\|Vector trimming]]		* [[Vector_trimming\|Vector trimming]]
	* [[Data_formats\|Data formats]]		* [[Data_formats\|Data formats]]

	* [[dpuiu_definitions\|Definitions]]		* [[dpuiu_definitions\|Definitions]]
	* [[dpuiu_meeting_notes\|Meeting notes]]		* [[dpuiu_meeting_notes\|Meeting notes]]
Line 95:		Line 94:
	* [[dpuiu_snp\|Snp calling]]		* [[dpuiu_snp\|Snp calling]]
	* [[dpuiu_todo\|ToDo]]		* [[dpuiu_todo\|ToDo]]

			* [[dpuiu_JHU\|JHU]]

	= CBCB software =		= CBCB software =