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专业背景：计算机科学研究方向与兴趣: JavaEE-Web软件开发, 生物信息学, 数据挖掘与机器学习, 智能信息系统目前工作: 基因组, 转录组, NGS高通量数据分析, 生物数据挖掘, 植物系统发育和比较进化基因组学

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http://illumina.ucr.edu/ht/documentation/analysis Data Analysis

2010-01-04 19:59:10| 分类：生信分析软件 | 标签： |举报 |字号大中小订阅

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http://illumina.ucr.edu/ht/documentation/analysis

Data Analysis

Sections

IIGB Bioinformatics Facility provides a wide variety of data analysis services. The following list provides only a general overview. To evaluate all data analysis options for the specific needs of a deep sequencing project, we strongly recommend to discuss them in a meeting with the bioinformatics core director, Thomas Girke.

Provided Data Formats

Click here for a description of the standard file formats provided for each sequencing run.

Quality Reports from Illumina Pipeline Software [PDF Manual]

QC of sequencing run
Quality filtering and adaptor trimming
Basic mapping to reference genome

Available Upon Request

Online genome browser support

Web BLAST server support

Custom Data Analyses

Comprehensive custom analysis: annotations, mapping, predictions etc.

Detailed data analysis reports
Statistical analysis

Please visit the Rates page for pricing information on these services.

UCR Manual on HT-Seq Data Analysis

ChIP-seq Analysis

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 Readshttp://amos.sourceforge.net/

More on this see: "Steven Salzberg assembling genomes from next-generation sequencers"

Digital Gene Expression (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

http://seqanswers.com

Google Solexa Group: http://groups.google.com/group/solexa?lnk=srg

Genographia next-generation genomics community: No longer online

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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