Data Analysis

Sections

• IIGB Services
• Manuals
  
• Software
• Links
• Publications

IIGB Services

The 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. 

• 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

Manuals

• UCR Manual on HT-Seq Data Analysis
• ChIP-seq Analysis
  

Software

• 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 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]
  

• 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
  

• 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 (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/
  

• 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