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Genomic datasets are growing dramatically as the cost of sequencing continues to decline and small sequencing devices become available. Enormous community databases store and share these data with the research community, but some of these genomic data analysis problems require large-scale computational platforms to meet both the memory and computational requirements. These applications differ from scientific simulations that dominate the workload on high-end parallel systems today and place different requirements on programming support, software libraries and parallel architectural design. For example, they involve irregular communication patterns such as asynchronous updates to shared data structures. We consider several problems in high-performance genomics analysis, including alignment, profiling, clustering and assembly for both single genomes and metagenomes. We identify some of the common computational patterns or ‘motifs’ that help inform parallelization strategies and compare our motifs to some of the established lists, arguing that at least two key patterns, sorting and hashing, are missing. This article is part of a discussion meeting issue ‘Numerical algorithms for high-performance computational science’. 

Systematically reasoning about the fine-grained causes of events in a real-world distributed system is challenging. Causality, from the distributed systems literature, can be used to compute the causal history of an arbitrary event in a distributed system, but the event's causal history is an over-approximation of the true causes. Data provenance, from the database literature, precisely describes why a particular tuple appears in the output of a relational query, but data provenance is limited to the domain of static relational databases. In this paper, we present wat-provenance: a novel form of provenance that provides the benefits of causality and data provenance. Given an arbitrary state machine, wat-provenance describes why the state machine produces a particular output when given a particular input. This enables system developers to reason about the causes of events in real-world distributed systems. We observe that automatically extracting the wat-provenance of a state machine is often infeasible. Fortunately, many distributed systems components have simple interfaces from which a developer can directly specify wat-provenance using a technique we call wat-provenance specifications. Leveraging the theoretical foundations of wat-provenance, we implement a prototype distributed debugging framework called Watermelon.