Revision as of 15:22, 4 December 2008

Articles

Velvet

Velvet: Algorithms for De Novo Short Read Assembly Using De Bruijn Graphs Genome Res. Mar 2008
Project Web Site at EBI Current version: 0.6 02/06/2008: Velvet 0.6

Edena

De novo bacterial genome sequencing: millions of very short reads assembled on a desktop computer Genome Res. Apr 2008
Project Web Site Current verision: 2.1.1 03/17/2008

ALLPATHS

ALLPATHS : De novo assembly of whole-genome shotgun microreads Genome Res. Mar 2008

Others

SSAKE
VCAKE
SHARCGS
SeqMan Genome Assembler (SMGA) by DNAStar(commercial)
Euler-SR

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/

Software @ CBCB

Under /fs/sz-user-supported/Linux-x86_64/bin/

Denovo assembly

edena
ssake
velveth,velvetg

Read mapping

blat
maq
soap

@@ Line 22: / Line 22: @@
 * Euler-SR
+= Consensus calling and Structural variation =
-== 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://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]
-=== 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://genome.ucsc.edu/FAQ/FAQblat FAQ]
@@ Line 41: / Line 42: @@
    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://www.sanger.ac.uk/Users/lh3/maq-poster.pdf Maq Poster from Sanger]
@@ Line 62: / Line 63: @@
    maq assemble cns.cns ref.bfa aln.nt.map 2> cns.log
-=== RMAP ===
+== 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
-=== SHRiMP ===
+== SHRiMP ==
 * [http://compbio.cs.toronto.edu/shrimp/ Web site]
 * Commands: rmapper-cs , rmapper-ls, ...
-=== SeqMap ===
+== SeqMap ==
 * [http://biogibbs.stanford.edu/~jiangh/SeqMap/ SeqMap] developed at Stanford
 * allows up to five mixed substitutions and inserted/deleted nucleotides in the mapping
@@ Line 86: / Line 87: @@
    ...
-=== SOAP ===
+== SHORE ==
+* [http://1001genomes.org/downloads/ SHORE]
+== SOAP ==
 * [http://soap.genomics.org.cn/ Web site (China)]
 * [http://soap.genomics.org.cn/#Formatofoutput Formatofoutput]
@@ Line 94: / Line 98: @@
    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
    socs socs.pref
@@ Line 121: / Line 113: @@
-=== 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]

Short read sequencing: Difference between revisions

Revision as of 15:22, 4 December 2008

Contents

Articles

Velvet

Edena

ALLPATHS

Others

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

Software @ CBCB

Denovo assembly

Read mapping

Navigation menu

Short read sequencing: Difference between revisions

Revision as of 15:22, 4 December 2008

Articles

Velvet

Edena

ALLPATHS

Others

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

Software @ CBCB

Denovo assembly

Read mapping

Navigation menu

Search