Alexander V. Sirotkin

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

The lions share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online ( http://bioinf.spbau.ru/spades ). It is distributed as open source software.

Multi-queued network processors for packets with heterogeneous processing requirements

Modern network processors (NPs) increasingly deal with packets with heterogeneous processing requirements. In this work, we consider the fundamental problem of managing a bounded size buffer at the input queue of an NP. Incoming traffic consists of packets, each packet requiring several rounds of processing before it can be transmitted out of the queue. The objective is to maximize the total number of successfully transmitted packets. In such an environment, it is well known that Shortest-Remaining-Processing-Time (SRPT) first scheduling with push-out is optimal [1]. However, it is hard to implement both priority queueing (PQ) by remaining processing and the push-out mechanism simultaneously in an NP. We explore alternatives for this architecture, addressing the simplicity vs. performance system design tradeoffs. We design a simplified architecture and provide worst-case guarantees for its throughput performance in different settings. We also conduct a comprehensive simulation study that validates our results.

Pathset graphs: a novel approach for comprehensive utilization of paired reads in genome assembly.

One of the key advances in genome assembly that has led to a significant improvement in contig lengths has been improved algorithms for utilization of paired reads (mate-pairs). While in most assemblers, mate-pair information is used in a post-processing step, the recently proposed Paired de Bruijn Graph (PDBG) approach incorporates the mate-pair information directly in the assembly graph structure. However, the PDBG approach faces difficulties when the variation in the insert sizes is high. To address this problem, we first transform mate-pairs into edge-pair histograms that allow one to better estimate the distance between edges in the assembly graph that represent regions linked by multiple mate-pairs. Further, we combine the ideas of mate-pair transformation and PDBGs to construct new data structures for genome assembly: pathsets and pathset graphs.

FIFO queueing policies for packets with heterogeneous processing

We consider the problem of managing a bounded size First-In-First-Out (FIFO) queue buffer, where each incoming unit-sized packet requires several rounds of processing before it can be transmitted out. Our objective is to maximize the total number of successfully transmitted packets. We consider both push-out (when the policy is permitted to drop already admitted packets) and non-push-out cases. In particular, we provide analytical guarantees for the throughput performance of our algorithms. We further conduct a comprehensive simulation study which experimentally validates the predicted theoretical behaviour.

A taxonomy of Semi-FIFO policies

Modern network processors (NPs) increasingly deal with packets that require heterogeneous processing. We consider the problem of managing a bounded size input queue buffer where each packet requires several rounds of processing before it can be transmitted out. The goal of admission control policies is to maximize the total number of successfully transmitted packets. Usually the transmission order of the packets is induced by the processing order. However, processing order can have a significant impact on the performance of buffer management policies even if the order of transmission is fixed. For this reason we decouple processing order from transmission order and restrict our transmission order to First-In-First-Out (FIFO) but allow for different orders of packet processing, introducing the class of such policies as Semi-FIFO. In this work, we build a taxonomy of Semi-FIFO policies and provide worst case guarantees for different processing orders. We consider various special cases and properties of Semi-FIFO policies, e.g., greedy, work-conserving, lazy, and push-out policies, and show how these properties affect performance. Further, we conduct a comprehensive simulation study that validates our results.

Shared Memory Buffer Management for Heterogeneous Packet Processing

Packet processing increasingly involves heterogeneous requirements. We consider the well-known model of a shared memory switch with bounded-size buffer and generalize it in two directions. First, we consider unit-sized packets labeled with an output port and a processing requirement (i.e., packets with heterogeneous processing), maximizing the number of transmitted packets. We analyze the performance of buffer management policies under various characteristics via competitive analysis that provides uniform guarantees across traffic patterns (Borodin and El-Yaniv, 1998). We propose the Longest-Work-Drop policy and show that it is at most 2-competitive and at least sqrt 2}-competitive. Second, we consider another generalization, posed as an open problem in [10], where each unit-sized packet is labeled with an output port and intrinsic value, and the goal is to maximize the total value of transmitted packets. We show first results in this direction and define a scheduling policy that, as we conjecture, may achieve constant competitive ratio. We also present a comprehensive simulation study that validates our results.

Online Scheduling FIFO Policies with Admission and Push-Out

We consider the problem of managing a bounded size First-In-First-Out (FIFO) queue buffer, where each incoming unit-sized packet requires several rounds of processing before it can be transmitted out. Our objective is to maximize the total number of successfully transmitted packets. We consider both push-out (when a policy is permitted to drop already admitted packets) and non-push-out cases. We provide worst-case guarantees for the throughput performance of our algorithms, proving both lower and upper bounds on their competitive ratio against the optimal algorithm, and conduct a comprehensive simulation study that experimentally validates predicted theoretical behavior.

Essential Traffic Parameters for Shared Memory Switch Performance

Cloud applications bring new challenges to the design of network elements, in particular accommodating for the burstiness of traffic workloads. Shared memory switches represent the best candidate architecture to exploit buffer capacity; we analyze the performance of this architecture. Our goal is to explore the impact of additional traffic characteristics such as varying processing requirements and packet values on objective functions. The outcome of this work is a better understanding of the relevant parameters for buffer management to achieve better performance in dynamic environments of data centers. We consider a model that captures more of the properties of the target architecture than previous work and consider several scheduling and buffer management algorithms that are specifically designed to optimize its performance. In particular, we provide analytic guarantees for the throughput performance of our algorithms that are independent from specific distributions of packet arrivals. We furthermore report on a comprehensive simulation study which validates our analytic results.

Pathset graphs: a novel approach for comprehensive utilization of paired reads in genome assembly

One of the key advances in genome assembly that has led to a significant improvement in contig lengths has been utilization of paired reads (mate-pairs). While in most assemblers, mate-pair information is used in a post-processing step, the recently proposed Paired de Bruijn Graph (PDBG) approach incorporates the mate-pair information directly in the assembly graph structure. However, the PDBG approach faces difficulties when the variation in the insert sizes is high. To address this problem, we first transform mate-pairs into edge-pair histograms that allow one to better estimate the distance between edges in the assembly graph that represent regions linked by multiple mate-pairs. Further, we combine the ideas of mate-pair transformation and PDBGs to construct new data structures for genome assembly: pathsets and pathset graphs.

A programmable buffer management platform

Buffering architectures and policies for their efficient management constitute one of the core ingredients of a network architecture. However, despite strong incentives to experiment with, and deploy, new policies, the opportunities for alterating anything beyond minor elements of such policies are limited. In this work we introduce a new specification language, OpenQueue, that allows users to specify entire buffering architectures and policies conveniently through several comparators and simple functions. We show examples of buffer management policies in OpenQueue and empirically demonstrate its direct impact on performance in various settings.