Short read sequencing - Revision history

Dpuiu at 15:38, 4 December 2008

2008-12-04T15:38:52Z

← Older revision		Revision as of 15:38, 4 December 2008
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			DELETED !!!

	= Consensus calling and Structural variation =		= Consensus calling and Structural variation =

Dpuiu at 15:29, 4 December 2008

2008-12-04T15:29:40Z

← Older revision		Revision as of 15:29, 4 December 2008
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	blat -noHead -t=dna -q=dna -tileSize=10 -stepSize=3 Pa.1con Pa.seq Pa.blat		blat -noHead -t=dna -q=dna -tileSize=10 -stepSize=3 Pa.1con Pa.seq Pa.blat

	== MAQ ==		== MAQ * ==
	* [http://maq.sourceforge.net/ Maq Sourceforge]		* [http://maq.sourceforge.net/ Maq Sourceforge]
	* [http://www.sanger.ac.uk/Users/lh3/maq-poster.pdf Maq Poster from Sanger]		* [http://www.sanger.ac.uk/Users/lh3/maq-poster.pdf Maq Poster from Sanger]
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	* [http://1001genomes.org/downloads/ SHORE]		* [http://1001genomes.org/downloads/ SHORE]

	== SOAP ==		== SOAP * ==
	* [http://soap.genomics.org.cn/ Web site (China)]		* [http://soap.genomics.org.cn/ Web site (China)]
	* [http://soap.genomics.org.cn/#Formatofoutput Formatofoutput]		* [http://soap.genomics.org.cn/#Formatofoutput Formatofoutput]

Dpuiu at 15:26, 4 December 2008

2008-12-04T15:26:23Z

← Older revision		Revision as of 15:26, 4 December 2008
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	~~= Articles =~~

	~~== Velvet ==~~

	* [http://www.genome.org/cgi/content/abstract/18/5/821 Velvet: Algorithms for De Novo Short Read Assembly Using De Bruijn Graphs] Genome Res. Mar 2008
	* [http://www.ebi.ac.uk/~zerbino/velvet/ Project Web Site at EBI] Current version: 0.6 02/06/2008: Velvet 0.6

	~~== Edena ==~~

	* [http://www.genome.org/cgi/content/abstract/gr.072033.107v2 De novo bacterial genome sequencing: millions of very short reads assembled on a desktop computer] Genome Res. Apr 2008
	* [http://www.genomic.ch/edena.php Project Web Site] Current verision: 2.1.1 03/17/2008

	~~== ALLPATHS ==~~

	* [http://www.genome.org/cgi/content/abstract/gr.7337908v1 ALLPATHS : De novo assembly of whole-genome shotgun microreads] Genome Res. Mar 2008

	~~== Others ==~~
	* SSAKE
	* VCAKE
	* SHARCGS
	* [http://www.dnastar.com/products/SMGA.php SeqMan Genome Assembler (SMGA)] by DNAStar(commercial)
	* Euler-SR

	= Consensus calling and Structural variation =		= Consensus calling and Structural variation =

Dpuiu: /* Software @ CBCB */

2008-12-04T15:23:00Z

Software @ CBCB

← Older revision		Revision as of 15:23, 4 December 2008
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	* /fs/szdata/genomes/human_ncbi_build36/ NCBI build36.1 May 2006 (Current build is 36.3 March 2008)		* /fs/szdata/genomes/human_ncbi_build36/ NCBI build36.1 May 2006 (Current build is 36.3 March 2008)
	* /fs/szdata/genomes/human_celera_2001_Orig/		* /fs/szdata/genomes/human_celera_2001_Orig/

	~~= Software @ CBCB =~~

	~~Under /fs/sz-user-supported/Linux-x86_64/bin/~~

	~~== Denovo assembly ==~~

	* edena
	* ssake
	* velveth,velvetg

	~~== Read mapping ==~~

	* blat
	* maq
	* soap

Dpuiu at 15:22, 4 December 2008

2008-12-04T15:22:42Z

← Older revision		Revision as of 15:22, 4 December 2008
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	* Euler-SR		* Euler-SR

			= Consensus calling and Structural variation =

	=~~= 06/27/2008~~ Consensus calling and Structural variation ==

	* [http://www.ncbi.nlm.nih.gov/pubmed/18321888 Consensus generation and variant detection by Celera Assembler.]		* [http://www.ncbi.nlm.nih.gov/pubmed/18321888 Consensus generation and variant detection by Celera Assembler.]
	* [http://compbio.cs.toronto.edu/structvar/ Detecting Structural Variations, Brudno et al. ]		* [http://compbio.cs.toronto.edu/structvar/ Detecting Structural Variations, Brudno et al. ]

	=~~= 06/20/2008~~ Read Mapping Software ==		= Read Mapping Software =

	* [http://en.wikipedia.org/wiki/Sequence_alignment_software#Short-Read_Sequence_Alignment Short-Read_Sequence_Alignment programs]		* [http://en.wikipedia.org/wiki/Sequence_alignment_software#Short-Read_Sequence_Alignment Short-Read_Sequence_Alignment programs]

	=== BLAT ===		== BFAST ==
			* need to e-mail to author to get the code

			== BLAT ==
	* [http://www.genome.org/cgi/reprint/GR-2292Rv1 BLAT—The BLAST-Like Alignment Tool, Genome Research 2002]		* [http://www.genome.org/cgi/reprint/GR-2292Rv1 BLAT—The BLAST-Like Alignment Tool, Genome Research 2002]
	* [http://genome.ucsc.edu/FAQ/FAQblat FAQ]		* [http://genome.ucsc.edu/FAQ/FAQblat FAQ]
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	blat -noHead -t=dna -q=dna -tileSize=10 -stepSize=3 Pa.1con Pa.seq Pa.blat		blat -noHead -t=dna -q=dna -tileSize=10 -stepSize=3 Pa.1con Pa.seq Pa.blat

	=== MAQ ===		== MAQ ==
	* [http://maq.sourceforge.net/ Maq Sourceforge]		* [http://maq.sourceforge.net/ Maq Sourceforge]
	* [http://www.sanger.ac.uk/Users/lh3/maq-poster.pdf Maq Poster from Sanger]		* [http://www.sanger.ac.uk/Users/lh3/maq-poster.pdf Maq Poster from Sanger]
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	maq assemble cns.cns ref.bfa aln.nt.map 2> cns.log		maq assemble cns.cns ref.bfa aln.nt.map 2> cns.log

	=== RMAP ===		== RMAP ==
	* [http://rulai.cshl.edu/rmap/ RMAP] : designed for Illumina-Solexa		* [http://rulai.cshl.edu/rmap/ RMAP] : designed for Illumina-Solexa
	* Command: rmap		* Command: rmap
	rmap -m 3 -w 33 -c Pa.1con Pa.seq -o Pa.rmap		rmap -m 3 -w 33 -c Pa.1con Pa.seq -o Pa.rmap

	=== SHRiMP ===		== SHRiMP ==
	* [http://compbio.cs.toronto.edu/shrimp/ Web site]		* [http://compbio.cs.toronto.edu/shrimp/ Web site]
	* Commands: rmapper-cs , rmapper-ls, ...		* Commands: rmapper-cs , rmapper-ls, ...

	=== SeqMap ===		== SeqMap ==
	* [http://biogibbs.stanford.edu/~jiangh/SeqMap/ SeqMap] developed at Stanford		* [http://biogibbs.stanford.edu/~jiangh/SeqMap/ SeqMap] developed at Stanford
	* allows up to five mixed substitutions and inserted/deleted nucleotides in the mapping		* allows up to five mixed substitutions and inserted/deleted nucleotides in the mapping
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	...		...

	=== SOAP ===		== SHORE ==
			* [http://1001genomes.org/downloads/ SHORE]

			== SOAP ==
	* [http://soap.genomics.org.cn/ Web site (China)]		* [http://soap.genomics.org.cn/ Web site (China)]
	* [http://soap.genomics.org.cn/#Formatofoutput Formatofoutput]		* [http://soap.genomics.org.cn/#Formatofoutput Formatofoutput]
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	soap -v 5 -d Pa.1con -a Pa.seq -o Pa.soap		soap -v 5 -d Pa.1con -a Pa.seq -o Pa.soap

	~~=== SSAHA ===~~		== SOCS ==
	* [http://www.sanger.ac.uk/Software/analysis/SSAHA/ Web site(Sanger)]
	* Focused on exact, nearly exact matches
	* Does not find all the exact matches???
	* Example: Solexa 33bp ~30% of reads are not found

	~~=== ZOOM ===~~
	* [http://bioinformatics.oxfordjournals.org/cgi/content/full/24/21/2431 ZOOM]

	~~=== SHORE ===~~
	* [http://1001genomes.org/downloads/ SHORE]

	=== SOCS ===
	* ABI color space		* ABI color space
	socs socs.pref		socs socs.pref
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	0		0

	=== ~~BFAST~~ ===		== SOLiD ==
	* ~~need to e-mail to author to get~~ the ~~code~~		* [http://solidsoftwaretools.com/gf/project/corona/ SOLID System Analysis Pipeline Tool (Corona Lite)]

			== SSAHA ==
			* [http://www.sanger.ac.uk/Software/analysis/SSAHA/ Web site(Sanger)]
			* Focused on exact, nearly exact matches
			* Does not find all the exact matches???
			* Example: Solexa 33bp ~30% of reads are not found

	==~~= SOLiD =~~==		== ZOOM ==
	* [http://~~solidsoftwaretools~~.~~com~~/gf/~~project~~/~~corona~~/ ~~SOLID System Analysis Pipeline Tool (Corona Lite)~~]		* [http://bioinformatics.oxfordjournals.org/cgi/content/full/24/21/2431 ZOOM]

	=~~= 06/13/2008~~ Genome Resequencing ==		= Genome Resequencing =

	* [http://www.nature.com/nature/journal/v452/n7189/pdf/nature06884.pdf The complete genome of an individual by massively parallel DNA sequencing (J.Watson's genome) Nature April 2008]		* [http://www.nature.com/nature/journal/v452/n7189/pdf/nature06884.pdf The complete genome of an individual by massively parallel DNA sequencing (J.Watson's genome) Nature April 2008]

Dpuiu at 15:20, 4 December 2008

2008-12-04T15:20:19Z

← Older revision		Revision as of 15:20, 4 December 2008
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	= Articles =		= Articles =

	~~== 07/11/2008 Denovo short read assembly ==~~		== Velvet ==

	=== Velvet ===

	* [http://www.genome.org/cgi/content/abstract/18/5/821 Velvet: Algorithms for De Novo Short Read Assembly Using De Bruijn Graphs] Genome Res. Mar 2008		* [http://www.genome.org/cgi/content/abstract/18/5/821 Velvet: Algorithms for De Novo Short Read Assembly Using De Bruijn Graphs] Genome Res. Mar 2008
	* [http://www.ebi.ac.uk/~zerbino/velvet/ Project Web Site at EBI] Current version: 0.6 02/06/2008: Velvet 0.6		* [http://www.ebi.ac.uk/~zerbino/velvet/ Project Web Site at EBI] Current version: 0.6 02/06/2008: Velvet 0.6

	=== Edena ===		== Edena ==

	* [http://www.genome.org/cgi/content/abstract/gr.072033.107v2 De novo bacterial genome sequencing: millions of very short reads assembled on a desktop computer] Genome Res. Apr 2008		* [http://www.genome.org/cgi/content/abstract/gr.072033.107v2 De novo bacterial genome sequencing: millions of very short reads assembled on a desktop computer] Genome Res. Apr 2008
	* [http://www.genomic.ch/edena.php Project Web Site] Current verision: 2.1.1 03/17/2008		* [http://www.genomic.ch/edena.php Project Web Site] Current verision: 2.1.1 03/17/2008

	=== ALLPATHS ===		== ALLPATHS ==

	* [http://www.genome.org/cgi/content/abstract/gr.7337908v1 ALLPATHS : De novo assembly of whole-genome shotgun microreads] Genome Res. Mar 2008		* [http://www.genome.org/cgi/content/abstract/gr.7337908v1 ALLPATHS : De novo assembly of whole-genome shotgun microreads] Genome Res. Mar 2008

	=== Others ===		== Others ==
	* SSAKE		* SSAKE
	* VCAKE		* VCAKE

Dpuiu: /* 06/20/2008 Read Mapping Software */

2008-12-04T15:18:39Z

06/20/2008 Read Mapping Software

@@ Line 50: / Line 50: @@
 * Command: maq map ...
 * does ungapped alignment on unpaired reads
 === RMAP ===

Dpuiu: /* 06/20/2008 Read Mapping Software */

2008-12-04T15:16:53Z

06/20/2008 Read Mapping Software

← Older revision		Revision as of 15:16, 4 December 2008
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	* Can do nt:aa translation		* Can do nt:aa translation
	* Command: blat		* Command: blat
			blat -noHead -t=dna -q=dna -tileSize=10 -stepSize=3 Pa.1con Pa.seq Pa.blat

	=== MAQ ===		=== MAQ ===
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	* [http://rulai.cshl.edu/rmap/ RMAP] : designed for Illumina-Solexa		* [http://rulai.cshl.edu/rmap/ RMAP] : designed for Illumina-Solexa
	* Command: rmap		* Command: rmap
			rmap -m 3 -w 33 -c Pa.1con Pa.seq -o Pa.rmap

	=== SHRiMP ===		=== SHRiMP ===
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	* Commands: soap, soap.contig, soap_dealign, soap.huge, soap.short		* Commands: soap, soap.contig, soap_dealign, soap.huge, soap.short
	* can use qualities, do read trimming, use pair ends, RNA alignments		* can use qualities, do read trimming, use pair ends, RNA alignments
			soap -v 5 -d Pa.1con -a Pa.seq -o Pa.soap

	=== SSAHA ===		=== SSAHA ===
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	=== SOCS ===		=== SOCS ===
	* ABI color space		* ABI color space
			socs socs.pref
			more socs.pref
			Req.fa
			Seq_F3.csfasta
			Seq_F3_QV.qual
			out_prefix
			2
			1000
			2
			false
			true
			0

	=== BFAST ===		=== BFAST ===

Dpuiu: /* 07/04/2008 4th of July: no meeting */

2008-12-04T15:13:43Z

07/04/2008 4th of July: no meeting

← Older revision		Revision as of 15:13, 4 December 2008
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	* Euler-SR		* Euler-SR

	~~== 07/04/2008 4th of July: no meeting ==~~

	== 06/27/2008 Consensus calling and Structural variation ==		== 06/27/2008 Consensus calling and Structural variation ==

Dpuiu: /* 06/20/2008 Read Mapping Software */

2008-12-04T14:33:12Z

06/20/2008 Read Mapping Software

← Older revision		Revision as of 14:33, 4 December 2008
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	== 06/20/2008 Read Mapping Software ==		== 06/20/2008 Read Mapping Software ==

			* [http://en.wikipedia.org/wiki/Sequence_alignment_software#Short-Read_Sequence_Alignment Short-Read_Sequence_Alignment programs]

	=== BLAT ===		=== BLAT ===
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	* Uses FASTQ format		* Uses FASTQ format
	* Command: maq map ...		* Command: maq map ...
			* does ungapped alignment on unpaired reads

	=== RMAP ===		=== RMAP ===
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	=== ZOOM ===		=== ZOOM ===
	* [http://bioinformatics.oxfordjournals.org/cgi/content/full/24/21/2431 ZOOM]		* [http://bioinformatics.oxfordjournals.org/cgi/content/full/24/21/2431 ZOOM]

			=== SHORE ===
			* [http://1001genomes.org/downloads/ SHORE]

			=== SOCS ===
			* ABI color space

			=== BFAST ===
			* need to e-mail to author to get the code

			=== SOLiD ===
			* [http://solidsoftwaretools.com/gf/project/corona/ SOLID System Analysis Pipeline Tool (Corona Lite)]

	== 06/13/2008 Genome Resequencing ==		== 06/13/2008 Genome Resequencing ==