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, Christopher J. Fields, Naohisa Goto, Michael L. Heuer, and Peter M. Rice
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

Assembly

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

Jason R. Miller, Sergey Koren, 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