Oyola et al. BMC Genomics 2012, 13:1 http://www.biomedcentral.com/1471-2164/13/1 Authors’ contributions Research in the lab was carried out by SOO, MAQ and SC. Bioinformatic analyses were carried out by TDO, YG, GM and MM. The research was coordinated by BM and HPS. DPK, DJT, HPS and MAQ conceived the project. SOO wrote the paper. All authors read and approved the final manuscript. Competing interests The authors declare that they have no competing interests. Received: 26 August 2011 Accepted: 3 January 2012 Published: 3 January 2012 References 1. Doolittle RF: The grand assault. Nature 2002, 419(6906):493-494. 2. Gardner MJ, Hall N, Fung E, White O, Berriman M, Hyman RW, Carlton JM, Pain A, Nelson KE, Bowman S, et al: Genome sequence of the human malaria parasite Plasmodium falciparum. Nature 2002, 419(6906):498-511. 3. Dohm JC, Lottaz C, Borodina T, Himmelbauer H: Substantial biases in ultra-short read data sets from high-throughput DNA sequencing. Nucleic Acids Res 2008, 36(16):e105. 4. Aird D, Ross MG, Chen WS, Danielsson M, Fennell T, Russ C, Jaffe DB, Nusbaum C, Gnirke A: Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries. Genome Biol 2011, 12(2):R18. 5. Kieleczawa J, Mazaika E: Optimization of protocol for sequencing of difficult templates. J Biomol Tech 2010, 21(2):97-102. 6. Kozarewa I, Ning Z, Quail MA, Sanders MJ, Berriman M, Turner DJ: Amplification-free Illumina sequencing-library preparation facilitates improved mapping and assembly of (G+C)-biased genomes. Nat Methods 2009, 6(4):291-295. 7. Chevet E, Lemaitre G, Katinka MD: Low concentrations of tetramethylammonium chloride increase yield and specificity of PCR. Nucleic Acids Res 1995, 23(16):3343-3344. 8. Aurrecoechea C, Brestelli J, Brunk BP, Dommer J, Fischer S, Gajria B, Gao X, Gingle A, Grant G, Harb OS, et al: PlasmoDB: a functional genomic database for malaria parasites. Nucleic Acids Res 2009, , 37 Database: D539-543. 9. Carver T, Bohme U, Otto TD, Parkhill J, Berriman M: BamView: viewing mapped read alignment data in the context of the reference sequence. Bioinformatics 2010, 26(5):676-677. 10. Rutherford K, Parkhill J, Crook J, Horsnell T, Rice P, Rajandream MA, Barrell B: Artemis: sequence visualization and annotation. Bioinformatics 2000, 16(10):944-945. 11. Piepenburg O, Williams CH, Stemple DL, Armes NA: DNA detection using recombination proteins. PLoS Biol 2006, 4(7):e204. 12. Hoeijmakers WA, Bartfai R, Francoijs KJ, Stunnenberg HG: Linear amplification for deep sequencing. Nat Protoc 2011, 6(7):1026-1036. 13. Li H, Durbin R: Fast and accurate short read alignment with Burrows- Wheeler transform. Bioinformatics 2009, 25(14):1754-1760. 14. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R: The Sequence Alignment/Map format and SAMtools. Bioinformatics 2009, 25(16):2078-2079. 15. R-Development-Core-Team: A language and environment for statistical computing. In R: A Language and Environment for Statistical Computing.. Edited by: Computing RFfS. Vienna, Austria; 2010:. 16. Otto TD, Sanders M, Berriman M, Newbold C: Iterative Correction of Reference Nucleotides (iCORN) using second generation sequencing technology. Bioinformatics 2010, 26(14):1704-1707. doi:10.1186/1471-2164-13-1 Cite this article as: Oyola et al.: Optimizing illumina next-generation sequencing library preparation for extremely at-biased genomes. BMC Genomics 2012 13:1. Page 12 of 12 Submit your next manuscript to BioMed Central and take full advantage of: • Convenient online submission • Thorough peer review • No space constraints or color ﬁgure charges • Immediate publication on acceptance • Inclusion in PubMed, CAS, Scopus and Google Scholar • Research which is freely available for redistribution Submit your manuscript at www.biomedcentral.com/submit