Latest revision as of 15:38, 4 December 2008

DELETED !!!

Consensus calling and Structural variation

Read Mapping Software

Short-Read_Sequence_Alignment programs

BFAST

need to e-mail to author to get the code

BLAT

BLAT—The BLAST-Like Alignment Tool, Genome Research 2002
FAQ
Can align any type of reads
Can do nt:aa translation
Command: blat

 blat -noHead -t=dna  -q=dna  -tileSize=10 -stepSize=3 Pa.1con    Pa.seq    Pa.blat

MAQ *

Maq Sourceforge
Maq Poster from Sanger
Illumina-Solexa/AB-SOLiD , not 454 or capillary reads
Uses FASTQ format
Command: maq map ...
does ungapped alignment on unpaired reads

 SOLEXA
 maq.pl easyrun -d . ref.1con reads.fastq

 SOLID
 solid2fastq.pl reads_ shortname
 maq fastq2bfq shortname.fastq shortname.bfq
 maq fasta2csfa ref.fasta > ref.csfa
 maq fasta2bfa ref.csfa ref.csbfa
 maq fasta2bfa ref.fasta ref.bfa
 maq map -c aln.cs.map ref.csbfa shortname.bfq 2> aln.log
 maq csmap2nt aln.nt.map ref.bfa aln.cs.map
 maq assemble cns.cns ref.bfa aln.nt.map 2> cns.log

RMAP

RMAP : designed for Illumina-Solexa
Command: rmap

 rmap         -m 3 -w 33                            -c Pa.1con    Pa.seq -o Pa.rmap

SHRiMP

Web site
Commands: rmapper-cs , rmapper-ls, ...

SeqMap

SeqMap developed at Stanford
allows up to five mixed substitutions and inserted/deleted nucleotides in the mapping
allows sequences to contain N’s, and to have unequal lengths

 ./seqmap
 Usage: seqmap <number of mismatches> <probe FASTA file name> <transcript FASTA file name> <output file name> [options]
 
 Parameters:
 <number of mismatches>                          maximum edit distance allowed
 <probe FASTA file name>                         probe/tag/read sequences
 <transcript FASTA file name>                    reference sequences
 <output file name>                              name of the output file
 ...

SHORE

SHORE

SOAP *

Web site (China)
Formatofoutput
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

 soap         -v 5                                  -d Pa.1con -a Pa.seq -o Pa.soap

SOCS

ABI color space

 socs socs.pref
 more socs.pref
 Req.fa
 Seq_F3.csfasta
 Seq_F3_QV.qual
 out_prefix
 2
 1000
 2
 false
 true
 0

SOLiD

SOLID System Analysis Pipeline Tool (Corona Lite)

SSAHA

Web site(Sanger)
Focused on exact, nearly exact matches
Does not find all the exact matches???
Example: Solexa 33bp ~30% of reads are not found

ZOOM

ZOOM

Genome Resequencing

Whole-genome sequencing and variant discovery in C. elegans Nature Jan 2008

Links

1000 genomes

Chip-Seq @ Wikipedia

SRA
SRA FTP

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

June 14th 2008: Sept 19th 2008

 SRA001100       23      Illumina Genome Analyzer        BGI     1000Genomes Project Pilot 2     NA19240
 ...
 SRA002029       1       Illumina Genome Analyzer II     WUGSC   1000Genomes Project Pilot 2     NA19239

 /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

June 14th 2008: Sept 19th 2008

 SRA001037       2       454 GS FLX      BCM     1000Genomes Project Pilot 1     NA12812
 ...
 SRA001819       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/

@@ Line 1: / Line 1: @@
-= Articles =
+DELETED !!!
-== 06/13/2008 (Genome Resequencing) ==
+= Consensus calling and Structural variation =
-* [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]
+* [http://www.ncbi.nlm.nih.gov/pubmed/18321888 Consensus generation and variant detection by Celera Assembler.]
-* [http://www.nature.com/nature/journal/v452/n7189/extref/nature06884-s1.pdf J.Watson's genome (supplementary info) ]
+* [http://compbio.cs.toronto.edu/structvar/ Detecting Structural Variations, Brudno et al. ]
+= Read Mapping Software =
-* [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://en.wikipedia.org/wiki/Sequence_alignment_software#Short-Read_Sequence_Alignment Short-Read_Sequence_Alignment programs]
-== 06/20/2008 (Read Mapping Software)==
+== BFAST ==
+* need to e-mail to author to get the code
+== BLAT ==
 * [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://genome.ucsc.edu/FAQ/FAQblat FAQ]
+* Can align any type of reads
+* Can do nt:aa translation
+* Command: blat
+  blat -noHead -t=dna  -q=dna  -tileSize=10 -stepSize=3 Pa.1con    Pa.seq    Pa.blat
+== 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
+* Uses FASTQ format
+* Command: maq map ...
+* does ungapped alignment on unpaired reads
+  SOLEXA
+  maq.pl easyrun -d . ref.1con reads.fastq
+  SOLID
+  solid2fastq.pl reads_ shortname
+  maq fastq2bfq shortname.fastq shortname.bfq
+  maq fasta2csfa ref.fasta > ref.csfa
+  maq fasta2bfa ref.csfa ref.csbfa
+  maq fasta2bfa ref.fasta ref.bfa
+  maq map -c aln.cs.map ref.csbfa shortname.bfq 2> aln.log
+  maq csmap2nt aln.nt.map ref.bfa aln.cs.map
+  maq assemble cns.cns ref.bfa aln.nt.map 2> cns.log
-* [http://maq.sourceforge.net/ Map Sourceforge]
+== RMAP ==
+* [http://rulai.cshl.edu/rmap/ RMAP] : designed for Illumina-Solexa
+* Command: rmap
+  rmap         -m 3 -w 33                            -c Pa.1con    Pa.seq -o Pa.rmap
-* [http://rulai.cshl.edu/rmap/ RMAP]
+== SHRiMP ==
+* [http://compbio.cs.toronto.edu/shrimp/ Web site]
+* Commands: rmapper-cs , rmapper-ls, ...
-* [http://compbio.cs.toronto.edu/shrimp/ SHRiMP]
+== SeqMap ==
+* [http://biogibbs.stanford.edu/~jiangh/SeqMap/ SeqMap] developed at Stanford
+* allows up to five mixed substitutions and inserted/deleted nucleotides in the mapping
+* allows sequences to contain N’s, and to have unequal lengths
-* [http://soap.genomics.org.cn/ SOAP web site (China)]
+  ./seqmap
+  Usage: seqmap <number of mismatches> <probe FASTA file name> <transcript FASTA file name> <output file name> [options]
+  Parameters:
+  <number of mismatches>                          maximum edit distance allowed
+  <probe FASTA file name>                         probe/tag/read sequences
+  <transcript FASTA file name>                    reference sequences
+  <output file name>                              name of the output file
+  ...
+== SHORE ==
+* [http://1001genomes.org/downloads/ SHORE]
+== SOAP * ==
+* [http://soap.genomics.org.cn/ Web site (China)]
+* [http://soap.genomics.org.cn/#Formatofoutput Formatofoutput]
 * [http://soap.genomics.org.cn/SOAP_paper.pdf 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
+  soap         -v 5                                  -d Pa.1con -a Pa.seq -o Pa.soap
+== SOCS ==
+* ABI color space
+  socs socs.pref
+  more socs.pref
+  Req.fa
+  Seq_F3.csfasta
+  Seq_F3_QV.qual
+  out_prefix
+  false
+  true
+== SOLiD ==
+* [http://solidsoftwaretools.com/gf/project/corona/ SOLID System Analysis Pipeline Tool (Corona Lite)]
+== SSAHA ==
+* [http://www.sanger.ac.uk/Software/analysis/SSAHA/ Web site(Sanger)]
+* Focused on exact, nearly exact matches
+* Does not find all the exact matches???
+* Example: Solexa 33bp  ~30% of reads are not found
+== ZOOM  ==
+* [http://bioinformatics.oxfordjournals.org/cgi/content/full/24/21/2431 ZOOM]
+= Genome Resequencing =
+* [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]
+* [http://www.nature.com/nature/journal/v452/n7189/extref/nature06884-s1.pdf J.Watson's genome (supplementary info) ]
+* [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 =
@@ Line 28: / Line 117: @@
 * [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://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]
@@ Line 59: / Line 150: @@
    SRA000318       14      Solexa 1G Genome Analyzer       SC      1000Genomes Project Pilot 2     NA12892
    SRA000319       1       Solexa 1G Genome Analyzer       SC      1000Genomes Project Pilot 1     NA12004
+June 14th 2008: Sept 19th 2008
+  SRA001100       23      Illumina Genome Analyzer        BGI     1000Genomes Project Pilot 2     NA19240
+  ...
+  SRA002029       1       Illumina Genome Analyzer II     WUGSC   1000Genomes Project Pilot 2     NA19239
    /fs/szdata/Solexa/1000genomes
+* Example SRR001113.seq :
+,058,926 47 bp sequences
+,402,398 contain at least 1 '.'
 == 454 ==
-* 1000 Genomes (June 14th 2008)
+* 1000 Genomes
+June 14th 2008
    Accession       #Runs   Instrument      Center  Study                           [Individual]
    SRA000302       121     454 GS FLX      BCM     1000Genomes Project Pilot 2     NA12878
@@ Line 71: / Line 172: @@
    SRA001036       1       454 GS FLX      BCM     1000Genomes Project Pilot 1     NA12812
    SRA001094       1       454 GS FLX      BCM     1000Genomes Project Pilot 2     NA12878
+June 14th 2008: Sept 19th 2008
+  SRA001037       2       454 GS FLX      BCM     1000Genomes Project Pilot 1     NA12812
+  ...
+  SRA001819       1       454 GS FLX      BCM     1000Genomes Project Pilot 2     NA12878
 == Refseq ==
@@ Line 76: / Line 182: @@
 * /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

Short read sequencing: Difference between revisions

Latest revision as of 15:38, 4 December 2008

Contents

Consensus calling and Structural variation

Read Mapping Software

BFAST

BLAT

MAQ *

RMAP

SHRiMP

SeqMap

SHORE

SOAP *

SOCS

SOLiD

SSAHA

ZOOM

Genome Resequencing

Links

Data

Solexa

454

Refseq

Navigation menu

Short read sequencing: Difference between revisions

Latest revision as of 15:38, 4 December 2008

Consensus calling and Structural variation

Read Mapping Software

BFAST

BLAT

MAQ *

RMAP

SHRiMP

SeqMap

SHORE

SOAP *

SOCS

SOLiD

SSAHA

ZOOM

Genome Resequencing

Links

Data

Solexa

454

Refseq

Navigation menu

Search