Short read sequencing: Difference between revisions
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* [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/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/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] | * [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 == | == 06/20/2008 == | ||
* [http:// | * [http://www.genome.org/cgi/reprint/GR-2292Rv1 BLAT—The BLAST-Like Alignment Tool, Genome Research 2002] | ||
* [http://maq.sourceforge.net/ Sourceforge | * [http://maq.sourceforge.net/ Map Sourceforge] | ||
* [http://rulai.cshl.edu/rmap/ RMAP] | * [http://rulai.cshl.edu/rmap/ RMAP] | ||
| Line 18: | Line 18: | ||
* [http://compbio.cs.toronto.edu/shrimp/ SHRiMP] | * [http://compbio.cs.toronto.edu/shrimp/ SHRiMP] | ||
* [http:// | * [http://soap.genomics.org.cn/ SOAP web site (China)] | ||
* [http://soap.genomics.org.cn/SOAP_paper.pdf SOAP: short oligonucleotide alignment program, Bioinformatics Jan 2008] | |||
= Other = | = Other = | ||
Ben's web sites | Ben's web sites | ||
* [http://www.cbcb.umd.edu/~langmead/solexa_1000genomes.html Ben's 1] | * [http://www.cbcb.umd.edu/~langmead/solexa_1000genomes.html Ben's 1] | ||
* [http://www.cbcb.umd.edu/~langmead/solexa_format.html Ben's 2] | * [http://www.cbcb.umd.edu/~langmead/solexa_format.html Ben's 2] | ||
= Software = | |||
Under /fs/sz-user-supported/Linux-x86_64/bin/ | |||
== Denovo assembly == | |||
* edena | |||
* velvetg, velveth | |||
== Read mapping == | |||
* blat | |||
* maq | |||
* soap | |||
Revision as of 13:14, 14 June 2008
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)
06/20/2008
Other
Ben's web sites
Software
Under /fs/sz-user-supported/Linux-x86_64/bin/
Denovo assembly
- edena
- velvetg, velveth
Read mapping
- blat
- maq
- soap