Short read sequencing: Difference between revisions
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=== BLAT === | === BLAT === | ||
* [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 FAQ] | * [http://genome.ucsc.edu/FAQ/FAQblat FAQ] | ||
* Can align any type of reads | |||
* Can do nt:aa translation | |||
* Command: blat [options] | |||
=== MAQ === | === MAQ === | ||
* [http://maq.sourceforge.net/ Maq Sourceforge] | |||
* [http://www.sanger.ac.uk/Users/lh3/maq-poster.pdf Maq Poster from Sanger] : | |||
* Illumina-Solexa/AB-SOLiD , not 454 or capillary reads | * Illumina-Solexa/AB-SOLiD , not 454 or capillary reads | ||
* Uses FASTQ format | * Uses FASTQ format | ||
* | * Command: map map [options] | ||
=== RMAP === | === RMAP === | ||
* [http://rulai.cshl.edu/rmap/ RMAP] : designed for Illumina-Solexa | * [http://rulai.cshl.edu/rmap/ RMAP] : designed for Illumina-Solexa | ||
* Command: rmap [options] | |||
=== SHRiMP === | === SHRiMP === | ||
Revision as of 15:07, 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)
BLAT
- BLAT—The BLAST-Like Alignment Tool, Genome Research 2002
- FAQ
- Can align any type of reads
- Can do nt:aa translation
- Command: blat [options]
MAQ
- Maq Sourceforge
- Maq Poster from Sanger :
- Illumina-Solexa/AB-SOLiD , not 454 or capillary reads
- Uses FASTQ format
- Command: map map [options]
RMAP
- RMAP : designed for Illumina-Solexa
- Command: rmap [options]
SHRiMP
SOAP
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