INF-BIOX120 H13 curriculum

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Required curriculum for credit students

The curriculum consists of these four papers:

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


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


Oshlack A, Robinson MD, Young MD.
Genome Biol. 2010;11(12):220
From RNA-seq reads to differential expression results. 


Flicek P, Birney E.
Nat Methods. 2009 Nov;6
Sense from sequence reads : methods for alignment and assembly 


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

RNA-Seq

Anders S et al.
Nat Protoc. 2013 Sep;8(9):1765-86
Count-based differential expression analysis of RNA sequencing data using R and Bioconductor

Iyer MK & Chinnaiyan AM.
Nat Biotechnol. 2011 Jul 11;29(7):599-600
RNA-Seq unleashed

Trapnell C et al.
Nat Protoc. 2012 Mar 1;7(3):562-78
Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

Assembly

Niranjan Nagarajan & Mihai Pop
Nature Reviews Genetics 14, 157-167
Sequence assembly demystified

Jason R. Miller, Sergey Koren and Granger Sutton
Genomics Volume 95, Issue 6, June 2010, Pages 315–327
Assembly algorithms for next-generation sequencing data

Adam M Phillippy, Michael C Schatz and Mihai Pop
Genome Biology 2008, 9:R55
Genome assembly forensics: finding the elusive mis-assembly

Statistical genomics

Goecks, Jeremy, et al. Genome Biol 11.8 (2010): R86 Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences

Sandve, Geir K., et al. Nucleic acids res. (2013) The Genomic HyperBrowser: an analysis web server for genome-scale data