BIOINFORMATICS APPLICATIONS NOTE doi:10.1093/bioinformatics/bts571 Genome analysis Advance Access publication September 27, 2012 Advanced Complex Trait Analysis

Motivation: The Genome-wide Complex Trait Analysis (GCTA) software package can quantify the contribution of genetic variation to phenotypic variation for complex traits. However, as those datasets of interest continue to increase in size, GCTA becomes increasingly computationally prohibitive. We present an adapted version, Advanced Complex Trait Analysis (ACTA), demonstrating dramatically improved performance. Results: We restructure the genetic relationship matrix (GRM) estima-tion phase of the code and introduce the highly optimized parallel Basic Linear Algebra Subprograms (BLAS) library combined with manual parallelization and optimization. We introduce the Linear Algebra PACKage (LAPACK) library into the restricted maximum like-lihood (REML) analysis stage. For a test case with 8999 individuals and 279 435 single nucleotide polymorphisms (SNPs), we reduce the total runtime, using a compute node with two multi-core Intel Nehalem CPUs, from 17 h to 11 min. Availability and implementation: The source code is fully available under the GNU Public License, along with Linux binaries. For more information se