1,721,061 research outputs found
MetaCon: unsupervised clustering of metagenomic contigs with probabilistic k-mers statistics and coverage
Full text linkSequencing technologies allow the sequencing of microbial communities directly from the environment without prior culturing. Because assembly typically produces only genome fragments, also known as contigs, it is crucial to group them into putative species for further taxonomic profiling and down-streaming functional analysis. Taxonomic analysis of microbial communities requires contig clustering, a process referred to as binning, that is still one of the most challenging tasks when analyzing metagenomic data. The major problems are the lack of taxonomically related genomes in existing reference databases, the uneven abundance ratio of species, sequencing errors, and the limitations due to binning contig of different lengths
Fast Entropic Profiler: An Information Theoretic Approach for the Discovery of Patterns in Genomes
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Enhanced Compression of k-Mer Sets with Counters via de Bruijn Graphs
Full text linkAn essential task in computational genomics involves transforming input sequences into their constituent k-mers. The quest for an efficient representation of k-mer sets is crucial for enhancing the scalability of bioinformatic analyses. One widely used method involves converting the k-mer set into a de Bruijn graph (dBG), followed by seeking a compact graph representation via the smallest path cover. This study introduces USTAR* (Unitig STitch Advanced constRuction), a tool designed to compress both a set of k-mers and their associated counts. USTAR leverages the connectivity and density of dBGs, enabling a more efficient path selection for constructing the path cover. The efficacy of USTAR is demonstrated through its application in compressing real read data sets. USTAR improves the compression achieved by UST (Unitig STitch), the best algorithm, by percentages ranging from 2.3% to 26.4%, depending on the k-mer size, and it is up to 7 x times faster
Beyond fixed-resolution alignment-free measures for mammalian enhancers sequence comparison
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