BamTools was written in C++, and is supported on Linux, Mac OSX and MS Windows. Source code and documentation are freely available at http://github.org/pezmaster31/bamtools.

High-quality and complete reference genome assemblies are fundamental for the application of genomics to biology, disease, and biodiversity conservation. However, such assemblies are only available for a few non-microbial species 1-4 . To address this issue, the international Genome 10K (G10K) consortium 5,6 has worked over a five-year period to evaluate and develop cost-effective methods for assembling the most accurate and complete reference genomes to date. Here we summarize these developments, introduce a set of quality standards, and present lessons learned from sequencing and assembling 16 species representing major vertebrate lineages (mammals, birds, reptiles, amphibians, teleost fishes and cartilaginous fishes). We confirm that long-read sequencing technologies are essential for maximizing genome quality and that unresolved complex repeats and haplotype heterozygosity are major sources of error in assemblies. Our new assemblies identify and correct substantial errors in some of the best historical reference genomes. Adopting these lessons, we have embarked on the Vertebrate Genomes Project (VGP), an effort to generate high-quality, complete reference genomes for all ~70,000 extant vertebrate species and help enable a new era of discovery across the life sciences.

Highlights d The Uganda Genome Resource comprises genetic and phenotypic data on 6,400 individuals d Ugandans show geographically correlated genetic substructure and complex admixture d The Uganda sequence panel substantially improves imputation in African populations d The Uganda Genome Resource enables novel discovery of loci associated with traits

SpeedSeq is an open-source genome analysis platform that accomplishes alignment, variant detection and functional annotation of a 50× human genome in 13 hours on a low-cost server, alleviating a bioinformatics bottleneck that typically demands weeks of computation with extensive hands-on expert involvement. SpeedSeq offers competitive or superior performance to current methods for detecting germline and somatic single nucleotide variants, indels, and structural variants, and includes novel functionality for streamlined interpretation.Technical advances in second-generation DNA sequencing technologies have reduced both the cost and time required to generate whole-genome sequencing (WGS) data, creating opportunities in healthcare and academic research to survey the human genome with unprecedented depth and scope. However, bottlenecks in computational processing and variant interpretation have hindered adoption of these technologies for time-sensitive and large-scale projects. Using a standard pipeline based on BWA 1 , GATK 2 , SAMtools 3 , and Picard, processing a 50× human genome from raw sequence data to variant calls on a 32-thread server requires 60-70 hours (Supplementary Note 1). Furthermore, distinguishing Users may view, print, copy, and download text and data-mine the content in such documents, for the purposes of academic research, subject always to the full Conditions of use