Short read sequencing: Difference between revisions
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* [http://www.genome.org/cgi/reprint/GR-2292Rv1 BLAT—The BLAST-Like Alignment Tool, Genome Research 2002] | * [http://www.genome.org/cgi/reprint/GR-2292Rv1 BLAT—The BLAST-Like Alignment Tool, Genome Research 2002] | ||
* [http://genome.ucsc.edu/FAQ/FAQblat BLAT FAQ] | |||
* [http://maq.sourceforge.net/ Map Sourceforge] | * [http://maq.sourceforge.net/ Map Sourceforge] | ||
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# [http://www.cbcb.umd.edu/~langmead/solexa_format.html Ben's 2] | # [http://www.cbcb.umd.edu/~langmead/solexa_format.html Ben's 2] | ||
* [ 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] | |||
= Data = | |||
== Solexa == | |||
* [ftp://ftp.sanger.ac.uk/pub/PRODUCTION_SOFTWARE/data_sets/suis_solexa/ Strep suis Solexa at Sanger] | |||
* [http://www.genomic.ch/edena/mw2Reads.seq.gz Staphylococcus aureus strain MW2 (edena paper)] | |||
* [ftp://ftp.ncbi.nlm.nih.gov/pub/TraceDB/misc/examples/solexa NCBI Solexa example data set] | |||
* Pseudomonas aeruginosa | |||
* Pseudomonas syringae | |||
* 1000 Genomes (June 14th 2008) | |||
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 = | = Software = | ||
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== Denovo assembly == | == Denovo assembly == | ||
* edena | * [http://www.genome.org/cgi/content/abstract/gr.7337908v1 ALLPATHS Genome Research March 2008] | ||
* | * [http://www.genomic.ch/edena.php edena] | ||
* [http://www.bcgsc.ca/platform/bioinfo/software/ssake SSAKE | |||
* [http://www.ebi.ac.uk/~zerbino/velvet/ velvet] | |||
== Read mapping == | == Read mapping == | ||
Revision as of 23:06, 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
Data
Solexa
- Strep suis Solexa at Sanger
- Staphylococcus aureus strain MW2 (edena paper)
- NCBI Solexa example data set
- Pseudomonas aeruginosa
- Pseudomonas syringae
- 1000 Genomes (June 14th 2008)
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
Under /fs/sz-user-supported/Linux-x86_64/bin/
Denovo assembly
- ALLPATHS Genome Research March 2008
- edena
- [http://www.bcgsc.ca/platform/bioinfo/software/ssake SSAKE
- velvet
Read mapping
- blat
- maq
- soap