Short read sequencing: Difference between revisions

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= Articles =
DELETED !!!


== 07/11/2008 Denovo short read assembly ==
= Consensus calling and Structural variation =
 
=== 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
* [http://www.ebi.ac.uk/~zerbino/velvet/ Project Web Site at EBI] Current version: 0.6 02/06/2008: Velvet 0.6
 
=== 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
* [http://www.genomic.ch/edena.php Project Web Site] Current verision: 2.1.1 03/17/2008
 
=== ALLPATHS ===
 
* [http://www.genome.org/cgi/content/abstract/gr.7337908v1 ALLPATHS : De novo assembly of whole-genome shotgun microreads] Genome Res. Mar 2008
 
=== Others ===
* SSAKE
* VCAKE
* SHARCGS
* [http://www.dnastar.com/products/SMGA.php SeqMan Genome Assembler (SMGA)] by DNAStar(commercial)
* Euler-SR
 
 
 
== 06/27/2008 Consensus calling and Structural variation ==


* [http://www.ncbi.nlm.nih.gov/pubmed/18321888 Consensus generation and variant detection by Celera Assembler.]
* [http://www.ncbi.nlm.nih.gov/pubmed/18321888 Consensus generation and variant detection by Celera Assembler.]
* [http://compbio.cs.toronto.edu/structvar/ Detecting Structural Variations, Brudno et al. ]
* [http://compbio.cs.toronto.edu/structvar/ Detecting Structural Variations, Brudno et al. ]


== 06/20/2008 Read Mapping Software ==
= Read Mapping Software =


* [http://en.wikipedia.org/wiki/Sequence_alignment_software#Short-Read_Sequence_Alignment Short-Read_Sequence_Alignment programs]
* [http://en.wikipedia.org/wiki/Sequence_alignment_software#Short-Read_Sequence_Alignment Short-Read_Sequence_Alignment programs]


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


=== MAQ ===
== MAQ * ==
* [http://maq.sourceforge.net/ Maq Sourceforge]
* [http://maq.sourceforge.net/ Maq Sourceforge]
* [http://www.sanger.ac.uk/Users/lh3/maq-poster.pdf Maq Poster from Sanger]  
* [http://www.sanger.ac.uk/Users/lh3/maq-poster.pdf Maq Poster from Sanger]  
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   maq assemble cns.cns ref.bfa aln.nt.map 2> cns.log
   maq assemble cns.cns ref.bfa aln.nt.map 2> cns.log


=== RMAP ===
== RMAP ==
* [http://rulai.cshl.edu/rmap/ RMAP] : designed for Illumina-Solexa
* [http://rulai.cshl.edu/rmap/ RMAP] : designed for Illumina-Solexa
* Command: rmap  
* Command: rmap  
   rmap        -m 3 -w 33                            -c Pa.1con    Pa.seq -o Pa.rmap
   rmap        -m 3 -w 33                            -c Pa.1con    Pa.seq -o Pa.rmap


=== SHRiMP ===
== SHRiMP ==
* [http://compbio.cs.toronto.edu/shrimp/ Web site]
* [http://compbio.cs.toronto.edu/shrimp/ Web site]
* Commands: rmapper-cs , rmapper-ls, ...
* Commands: rmapper-cs , rmapper-ls, ...


=== SeqMap ===
== SeqMap ==
* [http://biogibbs.stanford.edu/~jiangh/SeqMap/ SeqMap] developed at Stanford
* [http://biogibbs.stanford.edu/~jiangh/SeqMap/ SeqMap] developed at Stanford
* allows up to five mixed substitutions and inserted/deleted nucleotides in the mapping
* allows up to five mixed substitutions and inserted/deleted nucleotides in the mapping
Line 88: Line 66:
   ...
   ...


=== SOAP ===
== SHORE ==
* [http://1001genomes.org/downloads/ SHORE]
 
== SOAP * ==
* [http://soap.genomics.org.cn/ Web site (China)]  
* [http://soap.genomics.org.cn/ Web site (China)]  
* [http://soap.genomics.org.cn/#Formatofoutput Formatofoutput]
* [http://soap.genomics.org.cn/#Formatofoutput Formatofoutput]
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   soap        -v 5                                  -d Pa.1con -a Pa.seq -o Pa.soap
   soap        -v 5                                  -d Pa.1con -a Pa.seq -o Pa.soap


=== SSAHA ===
== SOCS ==
* [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]
 
=== SHORE ===
* [http://1001genomes.org/downloads/ SHORE]
 
=== SOCS ===
* ABI color space
* ABI color space
   socs socs.pref
   socs socs.pref
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   0
   0


=== BFAST ===
== SOLiD ==
* need to e-mail to author to get the code
* [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


=== SOLiD ===
== ZOOM  ==
* [http://solidsoftwaretools.com/gf/project/corona/ SOLID System Analysis Pipeline Tool (Corona Lite)]
* [http://bioinformatics.oxfordjournals.org/cgi/content/full/24/21/2431 ZOOM]


== 06/13/2008 Genome Resequencing ==
= 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/pdf/nature06884.pdf The complete genome of an individual by massively parallel DNA sequencing (J.Watson's genome) Nature April 2008]
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* /fs/szdata/genomes/human_ncbi_build36/ NCBI build36.1 May 2006 (Current build is 36.3 March 2008)
* /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/
* /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

Latest revision as of 15:38, 4 December 2008

DELETED !!!

Consensus calling and Structural variation

Read Mapping Software

BFAST

  • need to e-mail to author to get the code

BLAT

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

MAQ *

 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

SOAP *

 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

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

Genome Resequencing

Links

Data

Solexa

 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/
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