Short read sequencing

Articles

06/13/2008

• The complete genome of an individual by massively parallel DNA sequencing (J.Watson's genome) Nature April 2008
• J.Watson's genome (supplementary info)

• Whole-genome sequencing and variant discovery in C. elegans Nature Jan 2008

06/20/2008

• BLAT—The BLAST-Like Alignment Tool, Genome Research 2002
• BLAT FAQ

• Map Sourceforge

• RMAP

• SHRiMP

• SOAP web site (China)
• SOAP: short oligonucleotide alignment program, Bioinformatics Jan 2008

Links

• 1000 genomes

• Ben's web site 1
• Ben's web site 2

• SRA
• SRA FTP

Data

Solexa

• Strep suis Solexa at Sanger 36bp, ~49X coverage
• Staphylococcus aureus strain MW2 (edena paper) 35bp, ~47X coverage
• Pseudomonas aeruginosa: 33bp, ~43X coverage
• Pseudomonas syringae: 32bp, ~31X coverage
• 1000 Genomes (June 14th 2008): 48bp

 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

Software @ CBCB

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

Denovo assembly

• edena
• ssake
• velveth,velvetg

Read mapping

• blat
• maq
• soap