Alexander S. Kulikov

Bio: Alexander S. Kulikov is an academic researcher from Russian Academy of Sciences. The author has contributed to research in topics: Furoxan & Ionic liquid. The author has an hindex of 21, co-authored 148 publications receiving 13702 citations. Previous affiliations of Alexander S. Kulikov include National Research University – Higher School of Economics & St. Petersburg Department of Steklov Institute of Mathematics.

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

Abstract: The lion's 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.

An elementary proof of a 3n - o(n) lower bound on the circuit complexity of affine dispersers

Abstract: A Boolean function f: F2n → F2 is called an affine disperser of dimension d, if f is not constant on any affine subspace of F2n of dimension at least d. Recently Ben-Sasson and Kopparty gave an explicit construction of an affine disperser for sublinear d. The main motivation for studying such functions comes from extracting randomness from structured sources of imperfect randomness. In this paper, we show another application: we give a very simple proof of a 3n-o(n) lower bound on the circuit complexity (over the full binary basis) of affine dispersers for sublinear dimension. The same lower bound 3n-o(n) (but for a completely different function) was given by Blum in 1984 and is still the best known. The main technique is to substitute variables by linear functions. This way the function is restricted to an affine subspace of F2n. An affine disperser for sublinear dimension then guarantees that one can make n - o(n) such substitutions before the function degenerates. It remains to show that each such substitution eliminates at least 3 gates from a circuit.

A new approach to proving upper bounds for MAX-2-SAT

Abstract: In this paper we present a new approach to proving upper bounds for the maximum 2-satisfiability problem (MAX-2-SAT). We present a new 2K/5.5-time algorithm for MAX-2-SAT, where K is the number of clauses in an input formula. We also obtain a 2N/6 bound, where N is the number of variables in an input formula, for a particular case of MAX-2-SAT, where each variable appears in at most three 2-clauses. This immediately implies a 2N/6 bound, where N is the number of vertices in an input graph, for the independent set problem on 3-regular graphs. The key point of our improvement is a combined complexity measure for estimating the running time of an algorithm. By using a new complexity measure we are able to provide a much simpler proof of new upper bounds for MAX-2-SAT than proofs of previously known bounds.

A better-than-3n lower bound for the circuit complexity of an explicit function.

Abstract: We consider Boolean circuits over the full binary basis. We prove a (3+1/86)n-o(n) lower bound onthe size of such a circuit for an explicitly definedpredicate, namely an affine disperser for sublinear dimension. This improves the 3n-o(n) bound of Norbert Blum (1984).The proof is based on the gate elimination technique extended with the following three ideas. We generalize the computational model by allowing circuits to contain cycles, this in turn allows us to perform affine substitutions. We use a carefully chosen circuit complexity measure to track the progress of the gate elimination process. Finally, we use quadratic substitutions that may be viewed as delayed affine substitutions.

QUAST: quality assessment tool for genome assemblies

Abstract: Summary: Limitations of genome sequencing techniques have led to dozens of assembly algorithms, none of which is perfect. A number of methods for comparing assemblers have been developed, but none is yet a recognized benchmark. Further, most existing methods for comparing assemblies are only applicable to new assemblies of finished genomes; the problem of evaluating assemblies of previously unsequenced species has not been adequately considered. Here, we present QUAST—a quality assessment tool for evaluating and comparing genome assemblies. This tool improves on leading assembly comparison software with new ideas and quality metrics. QUAST can evaluate assemblies both with a reference genome, as well as without a reference. QUAST produces many reports, summary tables and plots to help scientists in their research and in their publications. In this study, we used QUAST to compare several genome assemblers on three datasets. QUAST tables and plots for all of them are available in the Supplementary Material, and interactive versions of these reports are on the QUAST website.

MEGAHIT: An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph

Abstract: Summary: MEGAHIT is a NGS de novo assembler for assembling large and complex metagenomics data in a time- and cost-efficient manner. It finished assembling a soil metagenomics dataset with 252Gbps in 44.1 hours and 99.6 hours on a single computing node with and without a GPU, respectively. MEGAHIT assembles the data as a whole, i.e., no pre-processing like partitioning and normalization was needed. When compared with previous methods (Chikhi and Rizk, 2012; Howe, et al., 2014) on assembling the soil data, MEGAHIT generated a 3-time larger assembly, with longer contig N50 and average contig length; furthermore, 55.8% of the reads were aligned to the assembly, giving a 4-fold improvement . Availability: The source code of MEGAHIT is freely available at https://github.com/voutcn/megahit under GPLv3 license. Contact: rb@l3-bioinfo.com, twlam@cs.hku.hk

MEGAHIT: An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph

Abstract: MEGAHIT is a NGS de novo assembler for assembling large and complex metagenomics data in a time- and cost-efficient manner. It finished assembling a soil metagenomics dataset with 252Gbps in 44.1 hours and 99.6 hours on a single computing node with and without a GPU, respectively. MEGAHIT assembles the data as a whole, i.e., it avoids pre-processing like partitioning and normalization, which might compromise on result integrity. MEGAHIT generates 3 times larger assembly, with longer contig N50 and average contig length than the previous assembly. 55.8% of the reads were aligned to the assembly, which is 4 times higher than the previous. The source code of MEGAHIT is freely available at this https URL under GPLv3 license.

MetaSPAdes: A new versatile metagenomic assembler

Abstract: While metagenomics has emerged as a technology of choice for analyzing bacterial populations, the assembly of metagenomic data remains challenging, thus stifling biological discoveries. Moreover, recent studies revealed that complex bacterial populations may be composed from dozens of related strains, thus further amplifying the challenge of metagenomic assembly. metaSPAdes addresses various challenges of metagenomic assembly by capitalizing on computational ideas that proved to be useful in assemblies of single cells and highly polymorphic diploid genomes. We benchmark metaSPAdes against other state-of-the-art metagenome assemblers and demonstrate that it results in high-quality assemblies across diverse data sets.

Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads.

Abstract: The Illumina DNA sequencing platform generates accurate but short reads, which can be used to produce accurate but fragmented genome assemblies. Pacific Biosciences and Oxford Nanopore Technologies DNA sequencing platforms generate long reads that can produce complete genome assemblies, but the sequencing is more expensive and error-prone. There is significant interest in combining data from these complementary sequencing technologies to generate more accurate "hybrid" assemblies. However, few tools exist that truly leverage the benefits of both types of data, namely the accuracy of short reads and the structural resolving power of long reads. Here we present Unicycler, a new tool for assembling bacterial genomes from a combination of short and long reads, which produces assemblies that are accurate, complete and cost-effective. Unicycler builds an initial assembly graph from short reads using the de novo assembler SPAdes and then simplifies the graph using information from short and long reads. Unicycler uses a novel semi-global aligner to align long reads to the assembly graph. Tests on both synthetic and real reads show Unicycler can assemble larger contigs with fewer misassemblies than other hybrid assemblers, even when long-read depth and accuracy are low. Unicycler is open source (GPLv3) and available at github.com/rrwick/Unicycler.