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

• Map Sourceforge

• RMAP

• SHRiMP

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

Other

• 1000 genomes

• Ben's web sites

1. Ben's 1
2. Ben's 2

• [ http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=table&f=run&m=data&s=run SRA]

Software

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

Denovo assembly

• edena
• velvetg, velveth

Read mapping

• blat
• maq
• soap