Genome2

From CSBLwiki

Revision as of 09:35, 26 September 2009 (view source) Igchoi (Talk | contribs) (New page: TBA) ← Older edit		Revision as of 15:12, 27 September 2010 (view source) Csbl (Talk | contribs) Newer edit →
Line 1:		Line 1:
-	TBA	+	==Basic Statistics==
		+	===''de novo'' assembly by velvet===
		+	#contig fragments: 14,702
		+	#ave. length: 182 bp, Min=31, Max=51,398
		+	#Sum: 2,674,691 nt. (2.6 Mbp)
		+	#80%: < 200 nt.
		+	===strategy===
		+	#assembling by 15 known ''Lactobacillus'' genomes
		+	==Softwares==
		+	*[http://seqanswers.com/forums/showthread.php?t=43 Related softwares & their links]
		+	*comparative
		+	#[http://maq.sourceforge.net/maq-man.shtml#download Maq] (Mapping and Assembly with Qualities)
		+	##[http://maq.sourceforge.net/maq-man.shtml Manual]
		+	#[http://amos.sourceforge.net/docs/pipeline/AMOScmp.html AMOScmp] Comparative assembly package
		+	#[http://soap.genomics.org.cn/ SOAP] Short Oligonucleotide Analysis Package
		+	*<i>de novo</i> assembly
		+	#de Bruijn graphs
		+	##velvet
		+	##abyss 1.0.5
		+	#suffix tree-based approach
		+	##QSRA
		+	##SSAKE
		+	##VCAKE
		+	#overlap-layout-consensus
		+	##edena
		+	#??
		+	##SHARCGS
		+	##ALLPATHS
		+	*<i>ab initio</i> assembly
		+	#[http://seq.cs.iastate.edu/ PCAP & CAP3] assembler
		+	#Phrap
		+	#ARACHNE
		+	#EULER
		+	#[http://amos.sourceforge.net/ amos-minimus2]
		+	#Newbler
		+	#wgs
		+	*alignment
		+	#[http://www.ebi.ac.uk/~guy/exonerate/ exonerate] a generic tool for sequence alignment
		+	#[http://manatee.sourceforge.net/index.shtml Manatee] Web-based annotation system
		+	#[http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=Download local blast] NCBI BLAST
		+
		+	==Links==
		+	===Scripts===
		+	*[http://www.genome.ou.edu/informatics.html Various Perl Scripts]
		+	===Etc===
		+	*NCBI [http://www.ncbi.nlm.nih.gov/Genomes/ Genomes]
		+	*[http://www.genoscope.cns.fr/spip/Lactobacillus-bulgaricus-whole.html ''Lactobacillus delbrueckii bulgaricus''] by Genoscope
		+	*[http://seqanswers.com/forums/showthread.php?t=21 Tech Summary: Illumina's Solexa Sequencing Technology]
		+	*Case stuides:
		+	#[http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000186 Gene-Boosted Assembly of a Novel Bacterial Genome from Very Short Reads]
		+	##[http://www.cbcb.umd.edu/research/SR-assembly-tutorial.shtml SR assembly Tutorial]
		+	#[http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1000139 High-Precision, Whole-Genome Sequencing of Laboratory Strains Facilitates Genetic Studies]
		+	#[http://www.genome.org/cgi/content/full/18/5/802 De novo bacterial genome sequencing: Millions of very short reads ...]
		+	#[http://genome.cshlp.org/content/18/2/324.full Short read fragment assembly of bacterial genomes...]
		+	#[http://dx.doi.org/10.1101/gr.079053.108 De novo fragment assembly with short mate-paired reads: Does the read length matter?] ([[media:GR2008.pdf|PDF]])
		+	*Solexa format & Fastq format
		+	#[http://seqanswers.com/forums/showthread.php?t=330 sequence quality in solexa format]
		+	*Benchmark papers
		+	#A Draft Genome Sequence of Pseudomonas syringae pv. tomato T1 Reveals a Type III Effector Repertoire Significantly Divergent from That of Pseudomonas syringae pv. tomato DC3000, MPMI(2008) ([[media:Mpmi-22-1-0052.pdf|PDF]])
		+	#[http://www.nature.com/ng/journal/v40/n8/full/ng.195.html High-throughput sequencing provides insights into genome variation and evolution in Salmonella Typhi, Nature Genetics (2008)]

---

Revision as of 15:12, 27 September 2010

Contents 1 Basic Statistics 1.1 de novo assembly by velvet 1.2 strategy 2 Softwares 3 Links 3.1 Scripts 3.2 Etc

Basic Statistics

de novo assembly by velvet

1. contig fragments: 14,702
2. ave. length: 182 bp, Min=31, Max=51,398
3. Sum: 2,674,691 nt. (2.6 Mbp)
4. 80%: < 200 nt.

strategy

1. assembling by 15 known Lactobacillus genomes

Softwares

• Related softwares & their links
• comparative

1. Maq (Mapping and Assembly with Qualities)
   1. Manual
2. AMOScmp Comparative assembly package
3. SOAP Short Oligonucleotide Analysis Package

• de novo assembly

1. de Bruijn graphs
   1. velvet
   2. abyss 1.0.5
2. suffix tree-based approach
   1. QSRA
   2. SSAKE
   3. VCAKE
3. overlap-layout-consensus
   1. edena
4. ??
   1. SHARCGS
   2. ALLPATHS

• ab initio assembly

1. PCAP & CAP3 assembler
2. Phrap
3. ARACHNE
4. EULER
5. amos-minimus2
6. Newbler
7. wgs

• alignment

1. exonerate a generic tool for sequence alignment
2. Manatee Web-based annotation system
3. local blast NCBI BLAST

Links

Scripts

• Various Perl Scripts

Etc

• NCBI Genomes
• Lactobacillus delbrueckii bulgaricus by Genoscope
• Tech Summary: Illumina's Solexa Sequencing Technology
• Case stuides:

1. Gene-Boosted Assembly of a Novel Bacterial Genome from Very Short Reads
   1. SR assembly Tutorial
2. High-Precision, Whole-Genome Sequencing of Laboratory Strains Facilitates Genetic Studies
3. De novo bacterial genome sequencing: Millions of very short reads ...
4. Short read fragment assembly of bacterial genomes...
5. De novo fragment assembly with short mate-paired reads: Does the read length matter? (PDF)

• Solexa format & Fastq format

1. sequence quality in solexa format

• Benchmark papers

1. A Draft Genome Sequence of Pseudomonas syringae pv. tomato T1 Reveals a Type III Effector Repertoire Significantly Divergent from That of Pseudomonas syringae pv. tomato DC3000, MPMI(2008) (PDF)
2. High-throughput sequencing provides insights into genome variation and evolution in Salmonella Typhi, Nature Genetics (2008)