INF-BIOX121 H14 curriculum
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
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
