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Compression algorithm for colored de Bruijn graphs [PDF]
Algorithms for Molecular Biology, 2023 A colored de Bruijn graph (also called a set of k-mer sets), is a set of k-mers with every k-mer assigned a set of colors. Colored de Bruijn graphs are used in a variety of applications, including variant calling, genome assembly, and database search ...
Amatur Rahman +2 more
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Buffering updates enables efficient dynamic de Bruijn graphs [PDF]
Computational and Structural Biotechnology Journal, 2021 Motivation: The de Bruijn graph has become a ubiquitous graph model for biological data ever since its initial introduction in the late 1990s. It has been used for a variety of purposes including genome assembly (Zerbino and Birney, 2008; Bankevich et al.
Jarno Alanko +4 more
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Succinct dynamic de Bruijn graphs. [PDF]
Bioinformatics, 2021 Abstract Motivation The de Bruijn graph is one of the fundamental data structures for analysis of high throughput sequencing data. In order to be applicable to population-scale studies, it is essential to build and store the graph in a space- and time-efficient manner.
Alipanahi B +4 more
europepmc +5 more sources
Bifrost: highly parallel construction and indexing of colored and compacted de Bruijn graphs [PDF]
Genome Biology, 2020 Memory consumption of de Bruijn graphs is often prohibitive. Most de Bruijn graph-based assemblers reduce the complexity by compacting paths into single vertices, but this is challenging as it requires the uncompacted de Bruijn graph to be available in ...
Guillaume Holley, Páll Melsted
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Applications of de Bruijn graphs in microbiome research
iMeta, 2022 High‐throughput sequencing has become an increasingly central component of microbiome research. The development of de Bruijn graph‐based methods for assembling high‐throughput sequencing data has been an important part of the broader adoption of ...
Xiaofang Jiang
exaly +2 more sources
Simplitigs as an efficient and scalable representation of de Bruijn graphs [PDF]
Genome Biology, 2021 de Bruijn graphs play an essential role in bioinformatics, yet they lack a universal scalable representation. Here, we introduce simplitigs as a compact, efficient, and scalable representation, and ProphAsm, a fast algorithm for their computation.
Karel Břinda +2 more
doaj +2 more sources
Lossless indexing with counting de Bruijn graphs. [PDF]
Genome Res, 2022 Abstract Sequencing data is rapidly accumulating in public repositories. Making this resource accessible for interactive analysis at scale requires efficient approaches for its storage and indexing. There have recently been remarkable advances in building compressed representations of annotated
Karasikov M +3 more
europepmc +6 more sources
Alignment- and reference-free phylogenomics with colored de Bruijn graphs [PDF]
Algorithms for Molecular Biology, 2020 Background The increasing amount of available genome sequence data enables large-scale comparative studies. A common task is the inference of phylogenies—a challenging task if close reference sequences are not available, genome sequences are incompletely
Roland Wittler
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Fully automated annotation of mitochondrial genomes using a cluster-based approach with de Bruijn graphs [PDF]
Frontiers in Genetics, 2023 A wide range of scientific fields, such as forensics, anthropology, medicine, and molecular evolution, benefits from the analysis of mitogenomic data. With the development of new sequencing technologies, the amount of mitochondrial sequence data to be ...
Lisa Fiedler +2 more
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Scalable, ultra-fast, and low-memory construction of compacted de Bruijn graphs with Cuttlefish 2 [PDF]
Genome Biology, 2022 The de Bruijn graph is a key data structure in modern computational genomics, and construction of its compacted variant resides upstream of many genomic analyses. As the quantity of genomic data grows rapidly, this often forms a computational bottleneck.
Jamshed Khan +3 more
doaj +2 more sources