{"repo":"leylabmpi/Struo2","free":true,"listed":false,"github":"https://github.com/leylabmpi/Struo2","clone":"git clone https://github.com/leylabmpi/Struo2.git","description":"Scalable creating/updating of metagenome profiling databases","language":"Jupyter Notebook","stars":62,"topics":["database","metagenomics","ngs","pipeline"],"license":"MIT","category":"databases-storage","readme_excerpt":"Struo2 ====== Struo2: a pipeline for building custom databases for common metagenome profilers \"Struo\" -- from the Latin: “I build” or “I gather” Version: 2.3.0 Authors: Nick Youngblut Maintainers: Nick Youngblut WARNING: the pipeline is still in development and could change substantially without warning! TOC Use the GitHub auto-generated TOC (top-left above the README). Citation Struo2 Youngblut, Nicholas D., and Ruth E. Ley. 2021. “Struo2: Efficient Metagenome Profiling Database Construction for Ever-Expanding Microbial Genome Datasets.” PeerJ 9 (September): e12198. https://doi.org/10.7717/peerj.12198 Struo (original) Cuesta-Zuluaga, Jacobo de la, Ruth E. Ley, and Nicholas D. Youngblut. 2019. \"Struo: A Pipeline for Building Custom Databases for Common Metagenome Profilers.\" Bioinformatics , November. https://doi.org/10.1093/bioinformatics/btz899 Overview Efficiently create/update custom databases for the following metagenome profilers: Kraken2 Bracken KrakenUniq HUMAnN3 You can also just use Struo2 for efficiently clustering genes via mmseqs and generating gene & gene-cluster databases that can be efficiently updated via mmseqs2. Changes from Version 1 Support for HUMAnN3 HUMAnN3 uses a much more updated version of UniRef and a new version of DIAMOND All coding sequences from all genomes are now clustered prior to annotation, and then the annotations (UniRef IDs, by default) are propagated to each member of each cluster. This is substantially faster than the per-genome anno","default_branch":null,"files":null,"tree":[],"storefront":"/r/leylabmpi","claimed":false,"request_supported":{"post":"https://gitbuyer.com/r/leylabmpi/Struo2/request-supported","requests":0},"note":"indexed from public GitHub; nothing is for sale on this page. Clone it from GitHub. Paid listings live at /search."}