Abstract: A computer application programming interface (API) for interacting with genomic data. Genomic data is stored by a genomic information provider using cloud-optimized, tabular structures in the form of genomic tables. A client computer may instruct, via API method calls, the genomic information provider to create a genomic table. Client computers may add genomic data to the genomic table via additional API method calls. A client computer may close the genomic table via an API method call. Once closed, client computers may retrieve genomic data based on genomic coordinates from the genomic table via API method calls. In this way, the transmission of genomic data via flat files can be avoided.

Abstract: Genomic sequencing is implemented for high throughput applications that can include short reads. In one example, whole-genome sequencing involves a method in which a subset of fragments of a target genome are selected as a random function, and each fragment is replicated into clones. The clones are ordered into clone contigs based on sets of overlapping clones, and potential read overlaps are determined from clone read data. The method can also involve reading local assemblies of contigs from regions smaller than a clone length and assembling the local assemblies into read sets, combining the assembled read sets into clone-sized regions and assembling the clone-sized regions, and assembling the clone-sized regions into clone contigs. Overlapping sets of clones and their ordering can be determined computationally from read data, with a high depth of clone coverage to provide a large number of boundaries on which the assemblies can be segmented into overlapping regions of pooled reads.