Short read sequencing: Difference between revisions

From Cbcb
Jump to navigation Jump to search
No edit summary
Line 1: Line 1:
= Articles =
= Articles =


== 06/13/2008 (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]
== 06/27/2008 (Consensus calling and structural variation)==
* [http://www.nature.com/nature/journal/v452/n7189/extref/nature06884-s1.pdf J.Watson's genome (supplementary info) ]
 
* [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://www.nature.com/nmeth/journal/v5/n2/full/nmeth.1179.html;jsessionid=DC518BCD8B2CACAE8AFFF7F70DD46902 Whole-genome sequencing and variant discovery in C. elegans Nature Jan 2008]


== 06/20/2008 (Read Mapping Software)==
== 06/20/2008 (Read Mapping Software)==
Line 38: Line 40:
* can use qualities, do read trimming, use pair ends, RNA alignments
* can use qualities, do read trimming, use pair ends, RNA alignments


== 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://compbio.cs.toronto.edu/structvar/ Detecting Structural Variations, Brudno et al. ]
 
== 06/13/2008 (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/extref/nature06884-s1.pdf J.Watson's genome (supplementary info) ]
 
* [http://www.nature.com/nmeth/journal/v5/n2/full/nmeth.1179.html;jsessionid=DC518BCD8B2CACAE8AFFF7F70DD46902 Whole-genome sequencing and variant discovery in C. elegans Nature Jan 2008]
 


= Links =
= Links =

Revision as of 18:22, 20 June 2008

Articles

06/27/2008 (Consensus calling and structural variation)



06/20/2008 (Read Mapping Software)

BLAT

MAQ

RMAP

  • RMAP : designed for Illumina-Solexa
  • Command: rmap

SHRiMP

  • Web site
  • Commands: rmapper-cs , rmapper-ls, ...

SOAP



06/13/2008 (Genome Resequencing)


Links

Data

Solexa

 Accession       #Runs   Instrument                      Center  Study                          [Individual]
 SRA000303       41      Solexa 1G Genome Analyzer       BI      1000Genomes Project Pilot 2     NA12878
 SRA000304       49      Solexa 1G Genome Analyzer       BI      1000Genomes Project Pilot 2     NA12891
 SRA000305       56      Solexa 1G Genome Analyzer       BI      1000Genomes Project Pilot 2     NA12892
 SRA000307       1       Solexa 1G Genome Analyzer       SC      1000Genomes Project Pilot 1     NA10851
 SRA000308       2       Solexa 1G Genome Analyzer       SC      1000Genomes Project Pilot 1     NA11993
 SRA000309       3       Solexa 1G Genome Analyzer       SC      1000Genomes Project Pilot 1     NA11995
 SRA000310       1       Solexa 1G Genome Analyzer       SC      1000Genomes Project Pilot 1     NA12006
 SRA000311       1       Solexa 1G Genome Analyzer       SC      1000Genomes Project Pilot 1     NA12044
 SRA000312       2       Solexa 1G Genome Analyzer       SC      1000Genomes Project Pilot 1     NA12156
 SRA000313       1       Solexa 1G Genome Analyzer       SC      1000Genomes Project Pilot 1     NA12414
 SRA000314       1       Solexa 1G Genome Analyzer       SC      1000Genomes Project Pilot 1     NA12776
 SRA000315       1       Solexa 1G Genome Analyzer       SC      1000Genomes Project Pilot 1     NA12828
 SRA000316       12      Solexa 1G Genome Analyzer       SC      1000Genomes Project Pilot 2     NA12878
 SRA000317       8       Solexa 1G Genome Analyzer       SC      1000Genomes Project Pilot 2     NA12891
 SRA000318       14      Solexa 1G Genome Analyzer       SC      1000Genomes Project Pilot 2     NA12892
 SRA000319       1       Solexa 1G Genome Analyzer       SC      1000Genomes Project Pilot 1     NA12004
 /fs/szdata/Solexa/1000genomes

454

  • 1000 Genomes (June 14th 2008)
 Accession       #Runs   Instrument      Center  Study                           [Individual]
 SRA000302       121     454 GS FLX      BCM     1000Genomes Project Pilot 2     NA12878
 SRA001032       2       454 GS FLX      BCM     1000Genomes Project Pilot 2     NA12878
 SRA001036       1       454 GS FLX      BCM     1000Genomes Project Pilot 1     NA12812
 SRA001094       1       454 GS FLX      BCM     1000Genomes Project Pilot 2     NA12878

Refseq

  • /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/

Software @ CBCB

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

Denovo assembly

  • edena
  • ssake
  • velveth,velvetg

Read mapping

  • blat
  • maq
  • soap