Short read sequencing: Difference between revisions

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== 06/20/2008 (Read Mapping Software)==
== 06/20/2008 (Read Mapping Software)==


=== BLAT : any reads ===
=== BLAT ===
* Any type of reads
* [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://www.genome.org/cgi/reprint/GR-2292Rv1 BLAT—The BLAST-Like Alignment Tool, Genome Research 2002]
=== MAQ ===
  * [http://genome.ucsc.edu/FAQ/FAQblat FAQ]
* Illumina-Solexa/AB-SOLiD , not 454 or capillary reads
* [http://maq.sourceforge.net/ Maq Sourceforge]
* [http://www.sanger.ac.uk/Users/lh3/maq-poster.pdf Maq Poster from Sanger] :


2. MAQ : Illumina-Solexa/AB-SOLiD , not 454 or capillary reads
=== RMAP ===
  * [http://maq.sourceforge.net/ Maq Sourceforge]
* [http://rulai.cshl.edu/rmap/ RMAP] : designed for Illumina-Solexa
  * [http://www.sanger.ac.uk/Users/lh3/maq-poster.pdf Maq Poster from Sanger] :


3. RMAP
=== SHRiMP ===
  * [http://rulai.cshl.edu/rmap/ RMAP] : designed for Illumina-Solexa
 
4. SHRiMP
* [http://compbio.cs.toronto.edu/shrimp/ Web site]
* [http://compbio.cs.toronto.edu/shrimp/ Web site]


5. SOAP
=== SOAP ===
* [http://soap.genomics.org.cn/ Web site (China)]
* [http://soap.genomics.org.cn/ Web site (China)]
* [http://soap.genomics.org.cn/SOAP_paper.pdf SOAP: short oligonucleotide alignment program, Bioinformatics Jan 2008]
* [http://soap.genomics.org.cn/SOAP_paper.pdf SOAP: short oligonucleotide alignment program, Bioinformatics Jan 2008]

Revision as of 14:57, 17 June 2008

Articles

06/13/2008 (Genome Resequencing)

06/20/2008 (Read Mapping Software)

BLAT

MAQ

RMAP

  • RMAP : designed for Illumina-Solexa

SHRiMP

SOAP

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