Short read sequencing: Difference between revisions
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= Articles = | = Articles = | ||
== 07/11/2008 Denovo short read assembly == | |||
=== Velvet === | |||
* [http://www.genome.org/cgi/content/abstract/18/5/821 Velvet: Algorithms for De Novo Short Read Assembly Using De Bruijn Graphs] Genome Res. Mar 2008 | |||
=== Edena === | |||
* [http://www.genome.org/cgi/content/abstract/gr.072033.107v2 De novo bacterial genome sequencing: millions of very short reads assembled on a desktop computer] Genome Res. Apr 2008 | |||
== 07/04/2008 4th of July: no meeting == | |||
== 06/27/2008 Consensus calling and Structural variation == | == 06/27/2008 Consensus calling and Structural variation == | ||
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* [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] | ||
= Links = | = Links = | ||
Revision as of 01:05, 28 June 2008
Articles
07/11/2008 Denovo short read assembly
Velvet
- Velvet: Algorithms for De Novo Short Read Assembly Using De Bruijn Graphs Genome Res. Mar 2008
Edena
- De novo bacterial genome sequencing: millions of very short reads assembled on a desktop computer Genome Res. Apr 2008
07/04/2008 4th of July: no meeting
06/27/2008 Consensus calling and Structural variation
- Consensus generation and variant detection by Celera Assembler.
- Detecting Structural Variations, Brudno et al.
06/20/2008 Read Mapping Software
BLAT
- BLAT—The BLAST-Like Alignment Tool, Genome Research 2002
- FAQ
- Can align any type of reads
- Can do nt:aa translation
- Command: blat
MAQ
- Maq Sourceforge
- Maq Poster from Sanger
- Illumina-Solexa/AB-SOLiD , not 454 or capillary reads
- Uses FASTQ format
- Command: maq map ...
RMAP
- RMAP : designed for Illumina-Solexa
- Command: rmap
SHRiMP
- Web site
- Commands: rmapper-cs , rmapper-ls, ...
SOAP
- Web site (China)
- SOAP: short oligonucleotide alignment program, Bioinformatics Jan 2008
- Commands: soap, soap.contig, soap_dealign, soap.huge, soap.short
- can use qualities, do read trimming, use pair ends, RNA alignments
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)
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
- Example SRR001113.seq :
7,058,926 47 bp sequences 2,402,398 contain at least 1 '.'
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