Courses / Workshops

• PreDoc Course, November 7 - 9, 2011 at EMBL Heidelberg, Germany
  Detecting Large-scale Genetic Variation in the Genome (predoc2011.pdf, handout2011.pdf)
• Metagenomics: From the Bench to Data Analysis, October 23 - 29, 2011 at EMBL Heidelberg, Germany
  Next Generation Sequencing Data Analysis (metagenomics.pdf)
• EMBL Master Course, July 18 - 20, 2011 at EMBL Heidelberg, Germany
  Variant Calling from Genomic Sequencing Data (variant.pdf, variant_slides.pdf)
• EMBL Master Course, June 14 - 18, 2011 at EMBL Heidelberg, Germany
  Target Enrichment and NGS (target.pdf)
• Bioinformatics Course, April 27, 2011 at Budweis, Czech Republic
  SNPs, Short InDels and Structural Variant Calling (budweis.pdf)
• PreDoc Course 2010, November 8 - 10, 2010 at EMBL Heidelberg, Germany
  Structural Variant Detection (predoc2010.pdf)
• Genome Capture and Next-Generation Sequencing, June 14 - 18, 2010 at EMBL Heidelberg, Germany
  Data Analysis for Genome Capture (capture.pdf, capslides.pdf)
• Advanced RNA-Seq and ChIP-Seq data analysis, June 7 - 9, 2010 at EMBL Heidelberg, Germany
  RNA-Seq, Short Read Alignment (rna_seq.pdf)
• Introductory workshop on bioinformatics for high-throughput sequencing, November 25 - 27, 2009 at EMBL Heidelberg, Germany
  Assembly (assembly.pdf)

Tutorials

• Linux, R Statistics and Awk Primer (primer.pdf)
• SAM/BAM Tutorial (sam.pdf, data.tar.gz)

Sequence Analysis Software, seqtools.tar.gz (*License)

• ./baseComp
  Calculates the base composition for each read position.
• ./baseQual
  Calculates the average base quality for each read position.
• ./insertSize
  Calculates the inner and outer insert-size as well as the strand-dependent and strand-independent read-pair orientation.
• ./stats
  Calculates mapped read statistics, redundancy, sequencing coverage, spanning coverage and basic insert size statistics.
• ./extract
  Extracts a single or multiple genomic intervals from a reference genome and outputs them as a multi-fasta file.
• ./cov
  Calculates the average or base-pair coverage for non-overlapping, overlapping or custom defined intervals.
• ./iover
  Annotates each reference interval (e.g., structural variant calls) with the overlap it shows to a set of query intervals (e.g., genes).

SeqAn

• SeqAn is an open source C++ library of efficient algorithms and data structures for the analysis of biological sequences. The most recent version of the library is available at www.seqan.de.

Publications

• Schwartzentruber J, Korshunov A, Liu XY, Jones DT, Pfaff E, Jacob K, Sturm D, Fontebasso AM, Quang DA, Tvnjes M, Hovestadt V, Albrecht S, Kool M, Nantel A, Konermann C, Lindroth A, Jaeger N, Rausch T, Ryzhova M, Korbel JO, Hielscher T, Hauser P, Garami M, Klekner A, Bognar L, Ebinger M, Schuhmann MU, Scheurlen W, Pekrun A, Fruehwald MC, Roggendorf W, Kramm C, Duerken M, Atkinson J, Lepage P, Montpetit A, Zakrzewska M, Zakrzewski K, Liberski PP, Dong Z, Siegel P, Kulozik AE, Zapatka M, Guha A, Malkin D, Felsberg J, Reifenberger G, von Deimling A, Ichimura K, Collins VP, Witt H, Milde T, Witt O, Zhang C, Castelo-Branco P, Lichter P, Faury D, Tabori U, Plass C, Majewski J, Pfister SM, Jabado N. Driver mutations in histone H3.3 and chromatin remodelling genes in paediatric glioblastoma. Nature. 2012.
• Rausch T, Jones DTW, Zapatka M, Stuetz AM, Zichner T, Weischenfeldt J, Jaeger N, Remke M, Shih D, Northcott PA, Pfaff E, Tica J, Wang Q, Massimi L, Witt H, Bender S, Pleier S, Cin H, Hawkins C, Beck C, Deimling A, Hans V, Brors B, Eils R, Scheurlen W, Blake J, Benes V, Kulozik AE, Witt O, Martin D, Zhang C, Porat R, Merino D, Wasserman J, Jabado N, Fontebasso A, Bullinger L, Ruecker F, Doehner K, Doehner H, Koster J, Molenaar JJ, Versteeg R, Kool M, Tabori U, Malkin D, Korshunov A, Taylor MD, Lichter P, Pfister SM, Korbel JO. Genome Sequencing of Pediatric Medulloblastoma Links Catastrophic DNA Rearrangements with TP53 Mutations. Cell. 2012.
• Mills RE, Walter K, Stewart C, Handsaker RE, Chen K, Alkan C, Abyzov A, Yoon SC, Ye K, Cheetham RK, Chinwalla A, Conrad DF, Fu Y, Grubert F, Hajirasouliha I, Hormozdiari F, Iakoucheva LM, Iqbal Z, Kang S, Kidd JM, Konkel MK, Korn J, Khurana E, Kural D, Lam HY, Leng J, Li R, Li Y, Lin CY, Luo R, Mu XJ, Nemesh J, Peckham HE, Rausch T, Scally A, Shi X, Stromberg MP, Stütz AM, Urban AE, Walker JA, Wu J, Zhang Y, Zhang ZD, Batzer MA, Ding L, Marth GT, McVean G, Sebat J, Snyder M, Wang J, Ye K, Eichler EE, Gerstein MB, Hurles ME, Lee C, McCarroll SA, Korbel JO; 1000 Genomes Project. Mapping copy number variation by population-scale genome sequencing. Nature. 2011 Feb 3;470(7332):59-65.
• Rausch T and Reinert K. Practical multiple sequence alignment, chapter in ''The problem solving handbook for computational biology and bioinformatics.''. Springer, 2010.
• Rausch T. Dissecting multiple sequence alignment methods. PhD thesis, Freie Universität Berlin, 2010.
• Emde AK and Rausch T. Multiple Alignment with Segments, chapter in ''Biological Sequence Analysis Using the SeqAn C++ Library''. CRC Press, Inc., 2009.
• Rausch T, Koren S, Denisov G, Weese D, Emde AK, Döring A and Reinert K. A consistency-based consensus algorithm for de novo and reference-guided sequence assembly of short reads. Bioinformatics, 25(9):1118-1124, 2009.
• Weese D, Emde AK, Rausch T, Döring A and Reinert K. RazerS - fast read mapping with sensitivity control. Genome Research, 19(9):1646-1654, 2009.
• Rausch T, Emde AK, Weese D, Döring A, Notredame C and Reinert K. Segment-based multiple sequence alignment. Bioinformatics, 24(16):i187-192, 2008.
• Rausch T, Emde AK and Reinert K. Robust consensus computation. BMC Bioinformatics, 9(Suppl 10):P4, 2008.
• Döring A, Weese D, Rausch T and Reinert K. SeqAn an efficient, generic C++ library for sequence analysis. BMC Bioinformatics, 9:11, 2008.
• Schulz MH, Weese D, Rausch T, Döring A, Reinert K and Vingron M. Fast and Adaptive Variable Order Markov Chain Construction. Proceedings of the 8th International Workshop in Algorithms in Bioinformatics (WABI'08), page 306-317. LNBI 5251, Publisher: Springer Verlag, 2008.