2 research outputs found
Synteny Paths for Assembly Graphs Comparison
Despite the recent developments of long-read sequencing technologies, it is still difficult to produce complete assemblies of eukaryotic genomes in an automated fashion. Genome assembly software typically output assembled fragments (contigs) along with assembly graphs, that encode all possible layouts of these contigs. Graph representation of the assembled genome can be useful for gene discovery, haplotyping, structural variations analysis and other applications. To facilitate the development of new graph-based approaches, it is important to develop algorithms for comparison and evaluation of assembly graphs produced by different software. In this work, we introduce synteny paths: maximal paths of homologous sequence between the compared assembly graphs. We describe Asgan - an algorithm for efficient synteny paths decomposition, and use it to evaluate assembly graphs of various bacterial assemblies produced by different approaches. We then apply Asgan to discover structural variations between the assemblies of 15 Drosophila genomes, and show that synteny paths are robust to contig fragmentation. The Asgan tool is freely available at: https://github.com/epolevikov/Asgan
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metaFlye: scalable long-read metagenome assembly using repeat graphs.
Long-read sequencing technologies have substantially improved the assemblies of many isolate bacterial genomes as compared to fragmented short-read assemblies. However, assembling complex metagenomic datasets remains difficult even for state-of-the-art long-read assemblers. Here we present metaFlye, which addresses important long-read metagenomic assembly challenges, such as uneven bacterial composition and intra-species heterogeneity. First, we benchmarked metaFlye using simulated and mock bacterial communities and show that it consistently produces assemblies with better completeness and contiguity than state-of-the-art long-read assemblers. Second, we performed long-read sequencing of the sheep microbiome and applied metaFlye to reconstruct 63 complete or nearly complete bacterial genomes within single contigs. Finally, we show that long-read assembly of human microbiomes enables the discovery of full-length biosynthetic gene clusters that encode biomedically important natural products