cortex_con has been used in the following publications

Genome Expansion and Gene Loss in Powdery Mildew Fungi Reveal Tradeoffs in Extreme Parasitism Spanu, P.D et al, Science 10 December 2010: Vol. 330 no. 6010 pp. 1543-1546

cortex_var has been used in the following publications

Whole Genome Sequencing for High-Resolution Investigation of Methicillin Resistant Staphylococcus aureus Epidemiology and Genome Plasticity SenGupta DJ, Cummings L, Hoogestraat DR, Butler-Wu SM, Shendure J, Cookson BT, Salipante SJ JCM doi:10.1128/JCM.00759-14

Novel Determinants of Antibiotic Resistance: Identification of Mutated Loci in Highly Methicillin-Resistant Subpopulations of Methicillin-Resistant Staphylococcus aureus Dordel J, Kim C, Chung M, Pardos de la Gándara M, Holden MTJ, Parkhill J, de Lencastre H, Bentley SD, Tomasz AmBio 5(2):e01000-13. doi:10.1128/mBio.01000-13.

Hundreds of SNPs for the Endangered pygmy hippopotamus (Choeropsis liberiensis) Senn H, O’Donoghue P, McEwing R, Ogden R Conservation Genetics Resources 2014

Genetic dissection of MAPK-mediated complex traits across S. cerevisiae Treusch S, Albert FW, Bloom JS, Kotenko I, Kruglyak L Biorxiv doi:

Single Nucleus Genome Sequencing Reveals High Similarity among Nuclei of an Endomycorrhizal Fungus Lin K, Limpens E, Zhang Z, Ivanov S, Saunders DGO, et al. PLoS Genet 10(1): e1004078.

Beyond genomic variation - comparison and functional annotation of three Brassica rapa genomes: a turnip, a rapid cycling and a Chinese cabbage Lin K, Zhang N, Severing E et al. BMC Genomics 2014, 15:250 zahara

Contributions of intrinsic mutation rate and selfish selection to levels of de novo HRAS mutations in the paternal germline. Giannoulatou E, McVean G, Taylor IB, McGowan SJ, Maher GJ et al. PNAS 10.1073/pnas.1311381110

Within-Host Evolution of Staphylococcus aureus during Asymptomatic Carriage. Golubchik T, Batty EM, Miller RR, Farr H, Young BC, et al. PLoS ONE. 8(5): e61319. doi:10.1371/journal.pone.0061319

Sturgeon conservation genomics: SNP discovery and validation using RAD sequencing. Congiu, L; Ogden, R; Gharbi, K; Mugue, N; Martinsohn, J; Senn, H; Davey, J.W; Pourkazemi, M; McEwing, R; Eland, C; Vidotto, M; Sergeev, A Mol Ecol. 2013 Jun;22(11):3112-23. doi: 10.1111/mec.12234

Reference-free SNP discovery for the Eurasian beaver from restriction site-associated DNA paired-end data. Senn H, Ogden R, Cezard T, Gharbi K, Iqbal Z, Johnson E, Kamps-Hughes N, Rosell F, McEwing R. Mol Ecol. 2013 Jun;22(11):3141-50. doi: 10.1111/mec.12242

High-throughput microbial population genomics using the Cortex variation assembler. Z Iqbal, I Turner, G McVean, Bioinformatics 2012; doi: 10.1093/bioinformatics/bts673

Evolutionary dynamics of Staphylococcus aureus during progression from carriage to disease. B. Young, T Golubchik et al, Proc. Nat. Acad. Sci Proc. Nat. Acad. Sci (2012) (doi:10.1073/pnas.1113219109)

De novo assembly and genotyping of variants using colored de Bruijn graphs. Z Iqbal(*), M Caccamo(*), I Turner, P Flicek, G McVean, Nature Genetics (2012) doi:10.1038/ng.1028 Access the recommendation on F1000

Mapping copy number variation by population-scale genome sequencing. Mills, R.E. et al, Nature 470,59-65 (2011)

A map of human genome variation from population-scale sequencing. The 1000 Genomes Consortium. Nature 467,1061-73 (2010)