10. Useful references

1. Dobin A, Davis CA, Schlesinger F, Drenkow J, Zaleski C, Jha S, Batut P, Chaisson M, Gingeras TR. STAR: ultrafast universal RNAAseq aligner. Bioinformatics. 2013 29(1):15A21.

2. Koboldt DC, Zhang Q, Larson DE, Shen D, McLellan MD, Lin L, Miller CA, Mardis ER, Ding L, Wilson RK. VarScan 2: somatic mutation and copy number alteration discovery in cancer by exome sequencing. Genome Res. 2012 22(3):568A76.

3. Langmead, B., Trapnell, C., Pop, M. & Salzberg, S. L. Ultrafast and memoryAefficient alignment of short DNA sequences to the human genome. Genome Biol. 10, R25 (2009).

4. Li H. and Durbin R. Fast and accurate short read alignment with BurrowsAWheeler Transform. Bioinformatics 2009, 25:1754A60.

5. Roberts, A., Pimentel, H., Trapnell, C. & Pachter, L. Identification of novel transcripts in annotated genomes using RNAASeq. Bioinformatics 27, 2325–2329 (2011).

6. Roberts, A., Trapnell, C., Donaghey, J., Rinn, J. L. & Pachter, L. Improving RNAASeq expression estimates by correcting for fragment bias. Genome Biol. 12, R22 (2011).

7. Trapnell, C., Pachter, L. & Salzberg, S. L. TopHat: discovering splice junctions with RNAA Seq. Bioinformatics 25, 1105–1111 (2009).

8. Trapnell, C. et al. Transcript assembly and quantification by RNASeq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol. 28, 511–515 (2010).

9. Zerbino DR, Birney E. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res. 2008 18(5):821A91

10. Zerbino DR. Using the Velvet de novo assembler for shortAread sequencing technologies. Curr Protoc Bioinformatics. 2010 Chapter 11:Unit 11.51