https://wiki.umiacs.umd.edu/cbcb/api.php?action=feedcontributions&feedformat=atom&user=Mschatz 2026-05-25T17:28:53Z User contributions MediaWiki 1.43.7 https://wiki.umiacs.umd.edu/cbcb/index.php?title=Short_read_sequencing&diff=3003 2008-06-20T18:23:10Z

<p>Mschatz: </p> <hr /> <div>= Articles =<br /> <br /> <br /> == 06/27/2008 Consensus calling and Structural variation ==<br /> <br /> * [http://www.ncbi.nlm.nih.gov/pubmed/18321888 Consensus generation and variant detection by Celera Assembler.]<br /> * [http://compbio.cs.toronto.edu/structvar/ Detecting Structural Variations, Brudno et al. ]<br /> <br /> <br /> <br /> <br /> == 06/20/2008 Read Mapping Software ==<br /> <br /> === BLAT ===<br /> * [http://www.genome.org/cgi/reprint/GR-2292Rv1 BLAT—The BLAST-Like Alignment Tool, Genome Research 2002]<br /> * [http://genome.ucsc.edu/FAQ/FAQblat FAQ]<br /> * Can align any type of reads<br /> * Can do nt:aa translation<br /> * Command: blat <br /> <br /> === MAQ ===<br /> * [http://maq.sourceforge.net/ Maq Sourceforge]<br /> * [http://www.sanger.ac.uk/Users/lh3/maq-poster.pdf Maq Poster from Sanger] <br /> * Illumina-Solexa/AB-SOLiD , not 454 or capillary reads<br /> * Uses FASTQ format<br /> * Command: maq map ...<br /> <br /> === RMAP ===<br /> * [http://rulai.cshl.edu/rmap/ RMAP] : designed for Illumina-Solexa<br /> * Command: rmap <br /> <br /> === SHRiMP ===<br /> * [http://compbio.cs.toronto.edu/shrimp/ Web site]<br /> * Commands: rmapper-cs , rmapper-ls, ...<br /> <br /> === SOAP ===<br /> * [http://soap.genomics.org.cn/ Web site (China)]<br /> * [http://soap.genomics.org.cn/SOAP_paper.pdf SOAP: short oligonucleotide alignment program, Bioinformatics Jan 2008]<br /> * Commands: soap, soap.contig, soap_dealign, soap.huge, soap.short<br /> * can use qualities, do read trimming, use pair ends, RNA alignments<br /> <br /> <br /> <br /> <br /> == 06/13/2008 Genome Resequencing ==<br /> <br /> * [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]<br /> * [http://www.nature.com/nature/journal/v452/n7189/extref/nature06884-s1.pdf J.Watson's genome (supplementary info) ]<br /> <br /> * [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]<br /> <br /> <br /> = Links =<br /> <br /> * [http://www.1000genomes.org/page.php?page=home 1000 genomes]<br /> <br /> * [http://www.cbcb.umd.edu/~langmead/solexa_1000genomes.html Ben's web site 1]<br /> * [http://www.cbcb.umd.edu/~langmead/solexa_format.html Ben's web site 2]<br /> <br /> * [http://en.wikipedia.org/wiki/Chip-Sequencing Chip-Seq @ Wikipedia]<br /> <br /> * [http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=table&amp;f=run&amp;m=data&amp;s=run SRA]<br /> * [ftp://ftp.ncbi.nih.gov/pub/TraceDB/ShortRead SRA FTP]<br /> <br /> = Data =<br /> <br /> == Solexa ==<br /> <br /> * [ftp://ftp.sanger.ac.uk/pub/PRODUCTION_SOFTWARE/data_sets/suis_solexa/ Strep suis Solexa at Sanger] 36bp, ~49X coverage<br /> * [http://www.genomic.ch/edena/mw2Reads.seq.gz Staphylococcus aureus strain MW2 (edena paper)] 35bp, ~47X coverage<br /> * Pseudomonas aeruginosa: 33bp, ~43X coverage<br /> * Pseudomonas syringae: 32bp, ~31X coverage<br /> * 1000 Genomes (June 14th 2008): 47bp<br /> <br /> Accession #Runs Instrument Center Study [Individual]<br /> SRA000303 41 Solexa 1G Genome Analyzer BI 1000Genomes Project Pilot 2 NA12878<br /> SRA000304 49 Solexa 1G Genome Analyzer BI 1000Genomes Project Pilot 2 NA12891<br /> SRA000305 56 Solexa 1G Genome Analyzer BI 1000Genomes Project Pilot 2 NA12892<br /> SRA000307 1 Solexa 1G Genome Analyzer SC 1000Genomes Project Pilot 1 NA10851<br /> SRA000308 2 Solexa 1G Genome Analyzer SC 1000Genomes Project Pilot 1 NA11993<br /> SRA000309 3 Solexa 1G Genome Analyzer SC 1000Genomes Project Pilot 1 NA11995<br /> SRA000310 1 Solexa 1G Genome Analyzer SC 1000Genomes Project Pilot 1 NA12006<br /> SRA000311 1 Solexa 1G Genome Analyzer SC 1000Genomes Project Pilot 1 NA12044<br /> SRA000312 2 Solexa 1G Genome Analyzer SC 1000Genomes Project Pilot 1 NA12156<br /> SRA000313 1 Solexa 1G Genome Analyzer SC 1000Genomes Project Pilot 1 NA12414<br /> SRA000314 1 Solexa 1G Genome Analyzer SC 1000Genomes Project Pilot 1 NA12776<br /> SRA000315 1 Solexa 1G Genome Analyzer SC 1000Genomes Project Pilot 1 NA12828<br /> SRA000316 12 Solexa 1G Genome Analyzer SC 1000Genomes Project Pilot 2 NA12878<br /> SRA000317 8 Solexa 1G Genome Analyzer SC 1000Genomes Project Pilot 2 NA12891<br /> SRA000318 14 Solexa 1G Genome Analyzer SC 1000Genomes Project Pilot 2 NA12892<br /> SRA000319 1 Solexa 1G Genome Analyzer SC 1000Genomes Project Pilot 1 NA12004<br /> <br /> /fs/szdata/Solexa/1000genomes<br /> <br /> == 454 ==<br /> <br /> * 1000 Genomes (June 14th 2008)<br /> <br /> Accession #Runs Instrument Center Study [Individual]<br /> SRA000302 121 454 GS FLX BCM 1000Genomes Project Pilot 2 NA12878<br /> SRA001032 2 454 GS FLX BCM 1000Genomes Project Pilot 2 NA12878<br /> SRA001036 1 454 GS FLX BCM 1000Genomes Project Pilot 1 NA12812<br /> SRA001094 1 454 GS FLX BCM 1000Genomes Project Pilot 2 NA12878<br /> <br /> == Refseq ==<br /> <br /> * /fs/szdata/genomes/human_ncbi_build36/ NCBI build36.1 May 2006 (Current build is 36.3 March 2008)<br /> * /fs/szdata/genomes/human_celera_2001_Orig/<br /> <br /> = Software @ CBCB =<br /> <br /> Under /fs/sz-user-supported/Linux-x86_64/bin/<br /> <br /> == Denovo assembly ==<br /> <br /> * edena<br /> * ssake<br /> * velveth,velvetg<br /> <br /> == Read mapping ==<br /> <br /> * blat<br /> * maq<br /> * soap</div>

Mschatz https://wiki.umiacs.umd.edu/cbcb/index.php?title=Short_read_sequencing&diff=3002 2008-06-20T18:22:18Z

<p>Mschatz: </p> <hr /> <div>= Articles =<br /> <br /> <br /> == 06/27/2008 (Consensus calling and structural variation)==<br /> <br /> * [http://www.ncbi.nlm.nih.gov/pubmed/18321888 Consensus generation and variant detection by Celera Assembler.]<br /> * [http://compbio.cs.toronto.edu/structvar/ Detecting Structural Variations, Brudno et al. ]<br /> <br /> <br /> <br /> <br /> == 06/20/2008 (Read Mapping Software)==<br /> <br /> === BLAT ===<br /> * [http://www.genome.org/cgi/reprint/GR-2292Rv1 BLAT—The BLAST-Like Alignment Tool, Genome Research 2002]<br /> * [http://genome.ucsc.edu/FAQ/FAQblat FAQ]<br /> * Can align any type of reads<br /> * Can do nt:aa translation<br /> * Command: blat <br /> <br /> === MAQ ===<br /> * [http://maq.sourceforge.net/ Maq Sourceforge]<br /> * [http://www.sanger.ac.uk/Users/lh3/maq-poster.pdf Maq Poster from Sanger] <br /> * Illumina-Solexa/AB-SOLiD , not 454 or capillary reads<br /> * Uses FASTQ format<br /> * Command: maq map ...<br /> <br /> === RMAP ===<br /> * [http://rulai.cshl.edu/rmap/ RMAP] : designed for Illumina-Solexa<br /> * Command: rmap <br /> <br /> === SHRiMP ===<br /> * [http://compbio.cs.toronto.edu/shrimp/ Web site]<br /> * Commands: rmapper-cs , rmapper-ls, ...<br /> <br /> === SOAP ===<br /> * [http://soap.genomics.org.cn/ Web site (China)]<br /> * [http://soap.genomics.org.cn/SOAP_paper.pdf SOAP: short oligonucleotide alignment program, Bioinformatics Jan 2008]<br /> * Commands: soap, soap.contig, soap_dealign, soap.huge, soap.short<br /> * can use qualities, do read trimming, use pair ends, RNA alignments<br /> <br /> <br /> <br /> <br /> == 06/13/2008 (Genome Resequencing) ==<br /> <br /> * [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]<br /> * [http://www.nature.com/nature/journal/v452/n7189/extref/nature06884-s1.pdf J.Watson's genome (supplementary info) ]<br /> <br /> * [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]<br /> <br /> <br /> = Links =<br /> <br /> * [http://www.1000genomes.org/page.php?page=home 1000 genomes]<br /> <br /> * [http://www.cbcb.umd.edu/~langmead/solexa_1000genomes.html Ben's web site 1]<br /> * [http://www.cbcb.umd.edu/~langmead/solexa_format.html Ben's web site 2]<br /> <br /> * [http://en.wikipedia.org/wiki/Chip-Sequencing Chip-Seq @ Wikipedia]<br /> <br /> * [http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=table&amp;f=run&amp;m=data&amp;s=run SRA]<br /> * [ftp://ftp.ncbi.nih.gov/pub/TraceDB/ShortRead SRA FTP]<br /> <br /> = Data =<br /> <br /> == Solexa ==<br /> <br /> * [ftp://ftp.sanger.ac.uk/pub/PRODUCTION_SOFTWARE/data_sets/suis_solexa/ Strep suis Solexa at Sanger] 36bp, ~49X coverage<br /> * [http://www.genomic.ch/edena/mw2Reads.seq.gz Staphylococcus aureus strain MW2 (edena paper)] 35bp, ~47X coverage<br /> * Pseudomonas aeruginosa: 33bp, ~43X coverage<br /> * Pseudomonas syringae: 32bp, ~31X coverage<br /> * 1000 Genomes (June 14th 2008): 47bp<br /> <br /> Accession #Runs Instrument Center Study [Individual]<br /> SRA000303 41 Solexa 1G Genome Analyzer BI 1000Genomes Project Pilot 2 NA12878<br /> SRA000304 49 Solexa 1G Genome Analyzer BI 1000Genomes Project Pilot 2 NA12891<br /> SRA000305 56 Solexa 1G Genome Analyzer BI 1000Genomes Project Pilot 2 NA12892<br /> SRA000307 1 Solexa 1G Genome Analyzer SC 1000Genomes Project Pilot 1 NA10851<br /> SRA000308 2 Solexa 1G Genome Analyzer SC 1000Genomes Project Pilot 1 NA11993<br /> SRA000309 3 Solexa 1G Genome Analyzer SC 1000Genomes Project Pilot 1 NA11995<br /> SRA000310 1 Solexa 1G Genome Analyzer SC 1000Genomes Project Pilot 1 NA12006<br /> SRA000311 1 Solexa 1G Genome Analyzer SC 1000Genomes Project Pilot 1 NA12044<br /> SRA000312 2 Solexa 1G Genome Analyzer SC 1000Genomes Project Pilot 1 NA12156<br /> SRA000313 1 Solexa 1G Genome Analyzer SC 1000Genomes Project Pilot 1 NA12414<br /> SRA000314 1 Solexa 1G Genome Analyzer SC 1000Genomes Project Pilot 1 NA12776<br /> SRA000315 1 Solexa 1G Genome Analyzer SC 1000Genomes Project Pilot 1 NA12828<br /> SRA000316 12 Solexa 1G Genome Analyzer SC 1000Genomes Project Pilot 2 NA12878<br /> SRA000317 8 Solexa 1G Genome Analyzer SC 1000Genomes Project Pilot 2 NA12891<br /> SRA000318 14 Solexa 1G Genome Analyzer SC 1000Genomes Project Pilot 2 NA12892<br /> SRA000319 1 Solexa 1G Genome Analyzer SC 1000Genomes Project Pilot 1 NA12004<br /> <br /> /fs/szdata/Solexa/1000genomes<br /> <br /> == 454 ==<br /> <br /> * 1000 Genomes (June 14th 2008)<br /> <br /> Accession #Runs Instrument Center Study [Individual]<br /> SRA000302 121 454 GS FLX BCM 1000Genomes Project Pilot 2 NA12878<br /> SRA001032 2 454 GS FLX BCM 1000Genomes Project Pilot 2 NA12878<br /> SRA001036 1 454 GS FLX BCM 1000Genomes Project Pilot 1 NA12812<br /> SRA001094 1 454 GS FLX BCM 1000Genomes Project Pilot 2 NA12878<br /> <br /> == Refseq ==<br /> <br /> * /fs/szdata/genomes/human_ncbi_build36/ NCBI build36.1 May 2006 (Current build is 36.3 March 2008)<br /> * /fs/szdata/genomes/human_celera_2001_Orig/<br /> <br /> = Software @ CBCB =<br /> <br /> Under /fs/sz-user-supported/Linux-x86_64/bin/<br /> <br /> == Denovo assembly ==<br /> <br /> * edena<br /> * ssake<br /> * velveth,velvetg<br /> <br /> == Read mapping ==<br /> <br /> * blat<br /> * maq<br /> * soap</div>

Mschatz https://wiki.umiacs.umd.edu/cbcb/index.php?title=Short_read_sequencing&diff=3001 2008-06-20T18:21:38Z

<p>Mschatz: /* 06/27/2008 (Consensus calling and structural variation) */</p> <hr /> <div>= Articles =<br /> <br /> == 06/13/2008 (Genome Resequencing) ==<br /> <br /> * [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]<br /> * [http://www.nature.com/nature/journal/v452/n7189/extref/nature06884-s1.pdf J.Watson's genome (supplementary info) ]<br /> <br /> * [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]<br /> <br /> == 06/20/2008 (Read Mapping Software)==<br /> <br /> === BLAT ===<br /> * [http://www.genome.org/cgi/reprint/GR-2292Rv1 BLAT—The BLAST-Like Alignment Tool, Genome Research 2002]<br /> * [http://genome.ucsc.edu/FAQ/FAQblat FAQ]<br /> * Can align any type of reads<br /> * Can do nt:aa translation<br /> * Command: blat <br /> <br /> === MAQ ===<br /> * [http://maq.sourceforge.net/ Maq Sourceforge]<br /> * [http://www.sanger.ac.uk/Users/lh3/maq-poster.pdf Maq Poster from Sanger] <br /> * Illumina-Solexa/AB-SOLiD , not 454 or capillary reads<br /> * Uses FASTQ format<br /> * Command: maq map ...<br /> <br /> === RMAP ===<br /> * [http://rulai.cshl.edu/rmap/ RMAP] : designed for Illumina-Solexa<br /> * Command: rmap <br /> <br /> === SHRiMP ===<br /> * [http://compbio.cs.toronto.edu/shrimp/ Web site]<br /> * Commands: rmapper-cs , rmapper-ls, ...<br /> <br /> === SOAP ===<br /> * [http://soap.genomics.org.cn/ Web site (China)]<br /> * [http://soap.genomics.org.cn/SOAP_paper.pdf SOAP: short oligonucleotide alignment program, Bioinformatics Jan 2008]<br /> * Commands: soap, soap.contig, soap_dealign, soap.huge, soap.short<br /> * can use qualities, do read trimming, use pair ends, RNA alignments<br /> <br /> == 06/27/2008 (Consensus calling and structural variation)==<br /> <br /> * [http://www.ncbi.nlm.nih.gov/pubmed/18321888 Consensus generation and variant detection by Celera Assembler.]<br /> * [http://compbio.cs.toronto.edu/structvar/ Detecting Structural Variations, Brudno et al. ]<br /> <br /> = Links =<br /> <br /> * [http://www.1000genomes.org/page.php?page=home 1000 genomes]<br /> <br /> * [http://www.cbcb.umd.edu/~langmead/solexa_1000genomes.html Ben's web site 1]<br /> * [http://www.cbcb.umd.edu/~langmead/solexa_format.html Ben's web site 2]<br /> <br /> * [http://en.wikipedia.org/wiki/Chip-Sequencing Chip-Seq @ Wikipedia]<br /> <br /> * [http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=table&amp;f=run&amp;m=data&amp;s=run SRA]<br /> * [ftp://ftp.ncbi.nih.gov/pub/TraceDB/ShortRead SRA FTP]<br /> <br /> = Data =<br /> <br /> == Solexa ==<br /> <br /> * [ftp://ftp.sanger.ac.uk/pub/PRODUCTION_SOFTWARE/data_sets/suis_solexa/ Strep suis Solexa at Sanger] 36bp, ~49X coverage<br /> * [http://www.genomic.ch/edena/mw2Reads.seq.gz Staphylococcus aureus strain MW2 (edena paper)] 35bp, ~47X coverage<br /> * Pseudomonas aeruginosa: 33bp, ~43X coverage<br /> * Pseudomonas syringae: 32bp, ~31X coverage<br /> * 1000 Genomes (June 14th 2008): 47bp<br /> <br /> Accession #Runs Instrument Center Study [Individual]<br /> SRA000303 41 Solexa 1G Genome Analyzer BI 1000Genomes Project Pilot 2 NA12878<br /> SRA000304 49 Solexa 1G Genome Analyzer BI 1000Genomes Project Pilot 2 NA12891<br /> SRA000305 56 Solexa 1G Genome Analyzer BI 1000Genomes Project Pilot 2 NA12892<br /> SRA000307 1 Solexa 1G Genome Analyzer SC 1000Genomes Project Pilot 1 NA10851<br /> SRA000308 2 Solexa 1G Genome Analyzer SC 1000Genomes Project Pilot 1 NA11993<br /> SRA000309 3 Solexa 1G Genome Analyzer SC 1000Genomes Project Pilot 1 NA11995<br /> SRA000310 1 Solexa 1G Genome Analyzer SC 1000Genomes Project Pilot 1 NA12006<br /> SRA000311 1 Solexa 1G Genome Analyzer SC 1000Genomes Project Pilot 1 NA12044<br /> SRA000312 2 Solexa 1G Genome Analyzer SC 1000Genomes Project Pilot 1 NA12156<br /> SRA000313 1 Solexa 1G Genome Analyzer SC 1000Genomes Project Pilot 1 NA12414<br /> SRA000314 1 Solexa 1G Genome Analyzer SC 1000Genomes Project Pilot 1 NA12776<br /> SRA000315 1 Solexa 1G Genome Analyzer SC 1000Genomes Project Pilot 1 NA12828<br /> SRA000316 12 Solexa 1G Genome Analyzer SC 1000Genomes Project Pilot 2 NA12878<br /> SRA000317 8 Solexa 1G Genome Analyzer SC 1000Genomes Project Pilot 2 NA12891<br /> SRA000318 14 Solexa 1G Genome Analyzer SC 1000Genomes Project Pilot 2 NA12892<br /> SRA000319 1 Solexa 1G Genome Analyzer SC 1000Genomes Project Pilot 1 NA12004<br /> <br /> /fs/szdata/Solexa/1000genomes<br /> <br /> == 454 ==<br /> <br /> * 1000 Genomes (June 14th 2008)<br /> <br /> Accession #Runs Instrument Center Study [Individual]<br /> SRA000302 121 454 GS FLX BCM 1000Genomes Project Pilot 2 NA12878<br /> SRA001032 2 454 GS FLX BCM 1000Genomes Project Pilot 2 NA12878<br /> SRA001036 1 454 GS FLX BCM 1000Genomes Project Pilot 1 NA12812<br /> SRA001094 1 454 GS FLX BCM 1000Genomes Project Pilot 2 NA12878<br /> <br /> == Refseq ==<br /> <br /> * /fs/szdata/genomes/human_ncbi_build36/ NCBI build36.1 May 2006 (Current build is 36.3 March 2008)<br /> * /fs/szdata/genomes/human_celera_2001_Orig/<br /> <br /> = Software @ CBCB =<br /> <br /> Under /fs/sz-user-supported/Linux-x86_64/bin/<br /> <br /> == Denovo assembly ==<br /> <br /> * edena<br /> * ssake<br /> * velveth,velvetg<br /> <br /> == Read mapping ==<br /> <br /> * blat<br /> * maq<br /> * soap</div>

Mschatz https://wiki.umiacs.umd.edu/cbcb/index.php?title=Short_read_sequencing&diff=3000 2008-06-20T18:14:56Z

<p>Mschatz: </p> <hr /> <div>= Articles =<br /> <br /> == 06/13/2008 (Genome Resequencing) ==<br /> <br /> * [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]<br /> * [http://www.nature.com/nature/journal/v452/n7189/extref/nature06884-s1.pdf J.Watson's genome (supplementary info) ]<br /> <br /> * [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]<br /> <br /> == 06/20/2008 (Read Mapping Software)==<br /> <br /> === BLAT ===<br /> * [http://www.genome.org/cgi/reprint/GR-2292Rv1 BLAT—The BLAST-Like Alignment Tool, Genome Research 2002]<br /> * [http://genome.ucsc.edu/FAQ/FAQblat FAQ]<br /> * Can align any type of reads<br /> * Can do nt:aa translation<br /> * Command: blat <br /> <br /> === MAQ ===<br /> * [http://maq.sourceforge.net/ Maq Sourceforge]<br /> * [http://www.sanger.ac.uk/Users/lh3/maq-poster.pdf Maq Poster from Sanger] <br /> * Illumina-Solexa/AB-SOLiD , not 454 or capillary reads<br /> * Uses FASTQ format<br /> * Command: maq map ...<br /> <br /> === RMAP ===<br /> * [http://rulai.cshl.edu/rmap/ RMAP] : designed for Illumina-Solexa<br /> * Command: rmap <br /> <br /> === SHRiMP ===<br /> * [http://compbio.cs.toronto.edu/shrimp/ Web site]<br /> * Commands: rmapper-cs , rmapper-ls, ...<br /> <br /> === SOAP ===<br /> * [http://soap.genomics.org.cn/ Web site (China)]<br /> * [http://soap.genomics.org.cn/SOAP_paper.pdf SOAP: short oligonucleotide alignment program, Bioinformatics Jan 2008]<br /> * Commands: soap, soap.contig, soap_dealign, soap.huge, soap.short<br /> * can use qualities, do read trimming, use pair ends, RNA alignments<br /> <br /> == 06/27/2008 (Consensus calling and structural variation)==<br /> <br /> * [http://www.ncbi.nlm.nih.gov/pubmed/18321888 Consensus generation and variant detection by Celera Assembler.]<br /> * In contact with Brudno<br /> <br /> = Links =<br /> <br /> * [http://www.1000genomes.org/page.php?page=home 1000 genomes]<br /> <br /> * [http://www.cbcb.umd.edu/~langmead/solexa_1000genomes.html Ben's web site 1]<br /> * [http://www.cbcb.umd.edu/~langmead/solexa_format.html Ben's web site 2]<br /> <br /> * [http://en.wikipedia.org/wiki/Chip-Sequencing Chip-Seq @ Wikipedia]<br /> <br /> * [http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=table&amp;f=run&amp;m=data&amp;s=run SRA]<br /> * [ftp://ftp.ncbi.nih.gov/pub/TraceDB/ShortRead SRA FTP]<br /> <br /> = Data =<br /> <br /> == Solexa ==<br /> <br /> * [ftp://ftp.sanger.ac.uk/pub/PRODUCTION_SOFTWARE/data_sets/suis_solexa/ Strep suis Solexa at Sanger] 36bp, ~49X coverage<br /> * [http://www.genomic.ch/edena/mw2Reads.seq.gz Staphylococcus aureus strain MW2 (edena paper)] 35bp, ~47X coverage<br /> * Pseudomonas aeruginosa: 33bp, ~43X coverage<br /> * Pseudomonas syringae: 32bp, ~31X coverage<br /> * 1000 Genomes (June 14th 2008): 47bp<br /> <br /> Accession #Runs Instrument Center Study [Individual]<br /> SRA000303 41 Solexa 1G Genome Analyzer BI 1000Genomes Project Pilot 2 NA12878<br /> SRA000304 49 Solexa 1G Genome Analyzer BI 1000Genomes Project Pilot 2 NA12891<br /> SRA000305 56 Solexa 1G Genome Analyzer BI 1000Genomes Project Pilot 2 NA12892<br /> SRA000307 1 Solexa 1G Genome Analyzer SC 1000Genomes Project Pilot 1 NA10851<br /> SRA000308 2 Solexa 1G Genome Analyzer SC 1000Genomes Project Pilot 1 NA11993<br /> SRA000309 3 Solexa 1G Genome Analyzer SC 1000Genomes Project Pilot 1 NA11995<br /> SRA000310 1 Solexa 1G Genome Analyzer SC 1000Genomes Project Pilot 1 NA12006<br /> SRA000311 1 Solexa 1G Genome Analyzer SC 1000Genomes Project Pilot 1 NA12044<br /> SRA000312 2 Solexa 1G Genome Analyzer SC 1000Genomes Project Pilot 1 NA12156<br /> SRA000313 1 Solexa 1G Genome Analyzer SC 1000Genomes Project Pilot 1 NA12414<br /> SRA000314 1 Solexa 1G Genome Analyzer SC 1000Genomes Project Pilot 1 NA12776<br /> SRA000315 1 Solexa 1G Genome Analyzer SC 1000Genomes Project Pilot 1 NA12828<br /> SRA000316 12 Solexa 1G Genome Analyzer SC 1000Genomes Project Pilot 2 NA12878<br /> SRA000317 8 Solexa 1G Genome Analyzer SC 1000Genomes Project Pilot 2 NA12891<br /> SRA000318 14 Solexa 1G Genome Analyzer SC 1000Genomes Project Pilot 2 NA12892<br /> SRA000319 1 Solexa 1G Genome Analyzer SC 1000Genomes Project Pilot 1 NA12004<br /> <br /> /fs/szdata/Solexa/1000genomes<br /> <br /> == 454 ==<br /> <br /> * 1000 Genomes (June 14th 2008)<br /> <br /> Accession #Runs Instrument Center Study [Individual]<br /> SRA000302 121 454 GS FLX BCM 1000Genomes Project Pilot 2 NA12878<br /> SRA001032 2 454 GS FLX BCM 1000Genomes Project Pilot 2 NA12878<br /> SRA001036 1 454 GS FLX BCM 1000Genomes Project Pilot 1 NA12812<br /> SRA001094 1 454 GS FLX BCM 1000Genomes Project Pilot 2 NA12878<br /> <br /> == Refseq ==<br /> <br /> * /fs/szdata/genomes/human_ncbi_build36/ NCBI build36.1 May 2006 (Current build is 36.3 March 2008)<br /> * /fs/szdata/genomes/human_celera_2001_Orig/<br /> <br /> = Software @ CBCB =<br /> <br /> Under /fs/sz-user-supported/Linux-x86_64/bin/<br /> <br /> == Denovo assembly ==<br /> <br /> * edena<br /> * ssake<br /> * velveth,velvetg<br /> <br /> == Read mapping ==<br /> <br /> * blat<br /> * maq<br /> * soap</div>

Mschatz