Short read sequencing: Difference between revisions
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* [http://www.cbcb.umd.edu/~langmead/solexa_1000genomes.html Ben's web site 1] | * [http://www.cbcb.umd.edu/~langmead/solexa_1000genomes.html Ben's web site 1] | ||
* [http://www.cbcb.umd.edu/~langmead/solexa_format.html Ben's web site 2] | * [http://www.cbcb.umd.edu/~langmead/solexa_format.html Ben's web site 2] | ||
* [http://en.wikipedia.org/wiki/Chip-Sequencing Chip-Seq @ Wikipedia] | |||
* [http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=table&f=run&m=data&s=run SRA] | * [http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=table&f=run&m=data&s=run SRA] | ||
* [ftp://ftp.ncbi.nih.gov/pub/TraceDB/ShortRead SRA FTP] | * [ftp://ftp.ncbi.nih.gov/pub/TraceDB/ShortRead SRA FTP] | ||
= Data = | = Data = | ||
Revision as of 14:37, 17 June 2008
Articles
06/13/2008 (Genome Resequencing)
- 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 (Read Mapping Software)
Links
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): 47bp
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