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
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
Data Processing Tools
Alignment Tools [ a more complete link page ]
De Novo Assembly of Short Reads
Comparative Assembly of Short Readshttp://amos.sourceforge.net/ More on this see: "Steven Salzberg assembling genomes from next-generation sequencers"
Digital Gene Expression (DGE)
Splice Junction Identification
R & Bioconductor
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