Is this you? As a journalist, you can create a free Muck Rack account to customize your profile, list your contact preferences, and upload a portfolio of your best work.
Claim your profile
Articles by Igor Martayan
Hyper-k-mers: efficient streaming k-mers representation
Abstract K-mers have become ubiquitous in modern bioinformatics pipelines. A key factor in their success is the ability to filter out erroneous k-mers by removing those with low abundances. However, large numbers of distinct k-mers make counting a memory-intensive step. Early tools addressed this issue by storing k-mers on disk. More recent solutions mitigate the excessive redundancy of overlapping k-mers by partially reassembling them into super-k-mers.
SimdMinimizers: Computing random minimizers, fast
Abstract Because of the rapidly-growing amount of sequencing data, computing sketches of large textual datasets has become an essential preprocessing task. These sketches are typically much smaller than the input sequences, but preserve sufficient information for downstream analysis. Minimizers are an especially popular sketching technique and used in a wide variety of applications. They sample at least one out of every w consecutive k-mers.
Brisk: Exact resource-efficient dictionary for k-mers
Abstract The rapid advancements in DNA sequencing technology have led to an unprecedented increase in the generation of genomic datasets, with modern sequencers now capable of producing up to ten terabases per run. However, the effective indexing and analysis of this vast amount of data pose significant challenges to the scientific community.
Hyper-k-mers: efficient streaming k-mers representation
Abstract K-mers have become ubiquitous in modern bioinformatics pipelines. A key factor in their success is the ability to filter out erroneous k-mers by removing those with low abundance. However, the vast number of distinct k-mers makes k-mer counting a significant resource bottleneck. Early tools addressed this issue by storing k-mers on disk. To mitigate the excessive redundancy caused by overlapping k-mers, super-k-mers were introduced, significantly decreasing memory usage.
Constrained enumeration of k-mers from a collection of references with metadata
Abstract While recent developments in k-mers indexing methods have opened up many new possibilities, they still have limitations in handling certain types of queries, such as identifying k-mers present in one dataset but absent in another. In this article, we present a framework for efficiently enumerating all k-mers within a collection of references that satisfy constraints related to their metadata tags.
Conway-Bromage-Lyndon (CBL): an exact, dynamic representation of k-mer sets
Abstract In this paper, we introduce the Conway-Bromage-Lyndon (CBL) structure, a compressed, dynamic and exact method for representing k-mer sets. Originating from Conway and Bromage's concept, CBL innovatively employs the smallest cyclic rotations of k-mers, akin to Lyndon words, to leverage lexicographic redundancies. In order to support dynamic operations and set operations, we propose a dynamic bit vector structure that draws a parallel with Elias-Fano's scheme.
Fractional Hitting Sets for Efficient and Lightweight Genomic Data Sketching
Thank you for your interest in spreading the word about bioRxiv. NOTE: Your email address is requested solely to identify you as the sender of this article. Your Email * Your Name * Send To * Enter multiple addresses on separate lines or separate them with commas. Message Subject (Your Name) has forwarded a page to you from bioRxiv Message Body (Your Name) thought you would like to see this page from the bioRxiv website.
Show More
loading
Actions
Is this you?
As a journalist, you can create a free Muck Rack account to customize your profile, list your contact preferences, and upload a portfolio of your best work.Get in touch with Igor
Contact Igor, search articles and posts on X, monitor coverage, and track replies from one place.
Learn more about Muck Rack