按最近已完成的 8 小时观测回合间的 GitHub 星标增量排序
Busabase is an open-source (MIT) database and workspace for AI agents — data, docs, skills, and apps in one place. Run it locally, self-host it inside your network, or use Busabase Cloud, and turn age
翻译准备中
Novelty-inclusive microbial (and now dsDNA phage) community profiling of shotgun metagenomes
翻译准备中
取自仓库 README
正在加载完整 README。 以下为已保存的摘录。
Welcome.
At heart, SingleM is a tool for profiling shotgun (both short and long-read) metagenomes. It shows good accuracy in estimating the relative abundances of community members, and has a particular strength in dealing with novel lineages.
It was originally designed to determine the relative abundance of bacterial and archaeal taxa in a sample. Microbial SingleM has been applied to ~700,000 public metagenomes. The resulting data are available at the Sandpiper companion website.查看完整 README ↗Welcome.
At heart, SingleM is a tool for profiling shotgun (both short and long-read) metagenomes. It shows good accuracy in estimating the relative abundances of community members, and has a particular strength in dealing with novel lineages.
It was originally designed to determine the relative abundance of bacterial and archaeal taxa in a sample. Microbial SingleM has been applied to ~700,000 public metagenomes. The resulting data are available at the Sandpiper companion website.
Recent versions have added features:
The method it uses also it suitable for some related tasks, such as assessing eukaryotic contamination, finding bias in genome recovery, and lineage-targeted MAG recovery. It can also be used as the basis for choosing metagenomes which, when coassembled, maximise the recovery of novel MAGs (see Bin Chicken).
Documentation can be found at https://wwood.github.io/singlem/.
Ben J. Woodcroft, Samuel T. N. Aroney, Rossen Zhao, Mitchell Cunningham, Joshua A. M. Mitchell, Rizky Nurdiansyah, Linda Blackall & Gene W. Tyson. Comprehensive taxonomic identification of microbial species in metagenomic data using SingleM and Sandpiper. Nat Biotechnol (2025). https://doi.org/10.1038/s41587-025-02738-1.
Raphael Eisenhofer, Antton Alberdi, Ben J. Woodcroft. Large-scale estimation of bacterial and archaeal DNA prevalence in metagenomes reveals biome-specific patterns. mSystems 0:e01062-25 (2026). https://doi.org/10.1128/msystems.01062-25.
Samuel T. N. Aroney, Rhys J. Newell, Gene W. Tyson and Ben J. Woodcroft, 2024. Bin Chicken: targeted metagenomic coassembly for the efficient recovery of novel genomes. Nat Methods 22, 2516–2524 (2025). https://doi.org/10.1038/s41592-025-02901-1
Rossen Zhao, Gene W. Tyson, Ben J. Woodcroft. Lyrebird: a tool for profiling dsDNA phage communities in metagenomic data. (in preparation).