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Data Analysis Software  

2012-05-04 04:54:43|  分类: 生物信息编程 |  标签: |举报 |字号 订阅

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Genome Browser
Using the Generic Genome Browser: general_help.html
Example genome browser showing S. cerevisiae (Yeast) chromosomes I and II: Click Here
NCBI's Sequence Viewer

Illumina Pipeline
Illumina Pipeline 1.5 Documentation: [FULL PDF Manual] [Quick Reference Booklet PDF]
Illumina Pipeline 1.3.2 Documentation: [Full PDF Manual] [Quick Reference Booklet PDF]
Illumina Pipeline 1.0 (old version) Documentation: http://illumina.ucr.edu/illumina_docs/; [PDF Manual]

Data Processing Tools
Alta-Cyclic base caller: http://hannonlab.cshl.edu/Alta-Cyclic/main.html
Phred, Phrap, Consed: http://www.phrap.org/phredphrapconsed.html
Rolexa probability base calling: http://bbcf.epfl.ch/view/BBCF/BBCFResources

Alignment Tools [ a more complete link page ]
Eland: http://illumina.ucr.edu/illumina_docs/
Maq (Mapping and Assembly with Quality): http://maq.sourceforge.net/maq-man.shtml
SOAP alignment tool: http://soap.genomics.org.cn/
SeqMaq: http://biogibbs.stanford.edu/~jiangh/SeqMap/
Bowtie: http://bowtie-bio.sourceforge.net/
Novoalign: http://www.novocraft.com
BWA - Burrows-Wheeler Alignment Tool: http://maq.sourceforge.net/bwa-man.shtml
BWA-SW (general purpose local alignment tool): http://i.cs.hku.hk/~ckwong3/bwtsw/
Zoom: http://www.bioinformaticssolutions.com/products/zoom/index.php
SHRiMP: http://compbio.cs.toronto.edu/shrimp/
SHORE (1001genomes.org): http://1001genomes.org/downloads/shore.html
CloudBurst (Highly Sensitive Short Read Mapping with MapReduce):http://apps.sourceforge.net/mediawiki/cloudburst-bio/index.php?title=CloudBurst
 
SNP Calling
SliderII: http://www.bcgsc.ca/platform/bioinfo/software/SliderII
Maq (Mapping and Assembly with Quality): http://maq.sourceforge.net/maq-man.shtml
SOAPsnp: http://soap.genomics.org.cn/
 
De Novo Assembly of Short Reads
Velvet: http://www.ebi.ac.uk/~zerbino/velvet/
ABySS: http://www.bcgsc.ca/platform/bioinfo/software/abyss
SOAPdenovo: http://soap.genomics.org.cn/soapdenovo.html
Edena: http://www.genomic.ch/edena.php (Hernandez et al 2008)
vcake (Hybrid 454 and Solexa): http://sourceforge.net/projects/vcake
SHARCGS: http://www.bcgsc.ca/bioinfo/software/ssake
QSRA: http://qsra.cgrb.oregonstate.edu (Bryant et al 2009)
 
Comparative Assembly of Short Reads
AMOScmp: http://amos.sourceforge.net/
More on this see: "Steven Salzberg assembling genomes from next-generation sequencers"
 
Digital Gene expression_r(DGE)
edgeR: Empirical analysis of digital gene expression data in R
 
RNA-Seq
ERANGE: http://woldlab.caltech.edu/rnaseq/
TopHat: http://tophat.cbcb.umd.edu/
HT-Seq Manual 
 
Splice Junction Identification
TopHat: http://tophat.cbcb.umd.edu/
 
R & Bioconductor
Biostrings: http://bioconductor.org/packages/2.2/bioc/html/Biostrings.html
ShortRead: http://www.bioconductor.org/packages/devel/bioc/html/ShortRead.html
TileQC: Web site; PubMed
 
Links
High Throughput Sequencing Forums
SEQanswers Froum: http://seqanswers.com
Google Solexa Group: http://groups.google.com/group/solexa?lnk=srg
Genographia next-generation genomics community: No longer online

Publications

Oxford Journals Next Generation Sequencing Article List: "A living resource that we will continually update to include the very latest papers in this area."
Bentley, D R, et al. (2008) Accurate whole human genome sequencing using reversible terminator chemistry. Nature, 456: 53-59. http://www.hubmed.org/display.cgi?uids=18987734
Dolan, P C, Denver, D R (2008) TileQC: a system for tile-based quality control of Solexa data. BMC Bioinformatics, 9: 250-250. http://www.hubmed.org/display.cgi?uids=18507856
Erlich, Y, Mitra, P P, delaBastide, M, McCombie, W R, Hannon, G J (2008) Alta-Cyclic: a self-optimizing base caller for next-generation sequencing. Nat Methods, 5: 679-682.http://www.hubmed.org/display.cgi?uids=18604217
Rougemont, J, Amzallag, A, Iseli, C, Farinelli, L, Xenarios, I, Naef, F (2008) Probabilistic base calling of Solexa sequencing data. BMC Bioinformatics, 9: 431-431.http://www.hubmed.org/display.cgi?uids=18851737
't Hoen, P A, Ariyurek, Y, Thygesen, H H, Vreugdenhil, E, Vossen, R H, de Menezes, R X, Boer, J M, van Ommen, G J, den Dunnen, J T (2008) Deep sequencing-based expression analysis shows major advances in robustness, resolution and inter-lab portability over five microarray platforms. Nucleic Acids Res, : . http://www.hubmed.org/display.cgi?uids=18927111
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