INF-BIOX121 H14 curriculum

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Required curriculum for credit students

The curriculum consists of these papers:

Sequencing technologies - the next generation
Metzker ML.
Nat Rev Genet. 2010 Jan;11(1):31-46

Tools for mapping high-throughput sequencing data
Fonseca NA, Rung J, Brazma A, Marioni JC.
Bioinformatics. 2012 Dec 15;28(24):3169-77.

A scaling normalization method for differential expression analysis of RNA-seq data.
Robinson MD, Oshlack A.
Genome Biol. 2010;11(3):R25.

Assembly algorithms for next-generation sequencing data
Miller JR, Koren S, Sutton G.
Genomics. 2010 Jun;95(6):315-27

ChIP-seq: advantages and challenges of a maturing technology
Park PJ.
Nat Rev Genet. 2009 Oct;10(10):669-80.

Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences
Goecks J, Nekrutenko A, Taylor J; Galaxy Team.
Genome Biol. 2010;11(8):R86.

The dilemma of choosing the ideal permutation strategy while estimating statistical significance of genome-wide enrichment
De S, Pedersen BS, Kechris K.
Brief Bioinform. 2013 Aug 16.

RNA-Seq: a revolutionary tool for transcriptomics
Wang Z, Gerstein M, Snyder M.
Nat Rev Genet. 2009 Jan;10(1):57-63

Genotype and SNP calling from next-generation sequencing data
Nielsen R, Paul JS, Albrechtsen A, Song YS.
Nat Rev Genet. 2011 Jun;12(6):443-51.

Suggested reading

File formats

SAM (and BAM): "Sequence Alignment/Map Format Specification" by "The SAM/BAM Format Specification Working Group"

FASTQ: Peter J. A. Cock et al
Nucleic Acids Res. 2010 April; 38(6): 1767–1771
The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants

Noble WS (2009) A Quick Guide to Organizing Computational Biology Projects. PLoS Comput Biol 5(7): e1000424. doi:10.1371/journal.pcbi.1000424

Wilson G, Aruliah DA, Brown CT, Chue Hong NP, Davis M, et al. (2014) Best Practices for Scientific Computing. PLoS Biol 12(1): e1001745. doi:10.1371/journal.pbio.1001745

Sandve GK, Nekrutenko A, Taylor J, Hovig E (2013) Ten Simple Rules for Reproducible Computational Research. PLoS Comput Biol 9(10): e1003285. doi:10.1371/journal.pcbi.1003285