2021年6月25日 · We developed SCAPP (Sequence Contents-Aware Plasmid Peeler)—an algorithm and tool to assemble plasmid sequences from metagenomic sequencing. SCAPP …

We propose a novel approach, PlasFlow, which uses a neural network-based model for the classification of metagenomic sequences and showed that it clearly outperforms cBar and …

2023年10月1日 · Long-read metagenomic sequencing could efficiently investigate the genetic contexts and host-species of ARGs. ARGs from Proteobacteria are commonly carried by …

2024年1月2日 · We introduce metaMDBG, a metagenomics assembler for PacBio HiFi reads. MetaMDBG combines a de Bruijn graph assembly in a minimizer space with an iterative …

We present the metaplasmidSPAdes tool for plasmid assembly in metagenomic data sets that reduced the false positive rate of plasmid detection compared with the state-of-the-art …

2020年4月3日 · We tested PlasClass sequence classification on held-out data and simulations, as well as publicly available bacterial isolates and plasmidome samples and plasmids assembled …

2022年6月2日 · We compiled a human metagenome assembled plasmid (MAP) database and interrogated differences across multiple studies that were originally designed to investigate the …

2023年9月21日 · With the growing availability of metagenomic sequencing data from different ecosystems, the development of efficient computational methods to accurately identify …

PlasFlow can recover plasmid se-quences from assembled metagenomes without any prior knowledge of the taxonomical or functional composition of samples with an accuracy up to …

2013年11月1日 · We selectively amplify plasmid DNA from an environmental sample. The method yields high quality and quantity plasmid DNA suited for deep sequencing. This method allows …