Short read sequencing: Difference between revisions

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= Articles =
= Articles =


== 07/11/2008 Denovo short read assembly ==
=== 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
=== 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
== 07/04/2008 4th of July: no meeting ==


== 06/27/2008 Consensus calling and Structural variation ==
== 06/27/2008 Consensus calling and Structural variation ==
Line 46: Line 57:


* [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]
* [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 01:05, 28 June 2008

Articles

07/11/2008 Denovo short read assembly

Velvet

Edena

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

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
  • Example SRR001113.seq :
 7,058,926 47 bp sequences
 2,402,398 contain at least 1 '.'

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