Discover our collection of 3 research tools and applications for plant biology.
Found 3 of 3 tools
The EDTA package was designed to filter out false discoveries in raw TE candidates and generate a high-quality non-redundant TE library for whole-genome TE annotations. Selection of initial search programs were based on benckmarkings on the annotation performance using a manually curated TE library in the rice genome.
Paralogs and off-target sequences improve phylogenetic resolution in a densely-sampled study of the breadfruit genus (Artocarpus, Moraceae). Recovering genes from targeted sequence capture data. Current version: 1.3.1 (August 2018). -- Read our article in Applications in Plant Sciences (Open Access). HybPiper was designed for targeted sequence capture, in which DNA sequencing libraries are enriched for gene regions of interest, especially for phylogenetics. HybPiper is a suite of Python scripts that wrap and connect bioinformatics tools in order to extract target sequences from high-throughput DNA sequencing reads.
Cuttlefish is a fast, parallel, and very lightweight memory tool to construct the compacted de Bruijn graph from genome reference(s). Cuttlefish is a tool for constructing the (colored) compacted de Bruijn graph from a collection of one or more genome references. Cuttlefish introduces a novel modeling scheme of the de Bruijn graph vertices as finite-state automata, and constrains the state-space for the automata to enable tracking of their transitioning states with very low memory usage. Cuttlefish is also fast and highly parallelizable. Experimental results demonstrate that the algorithm scales much better than existing approaches, especially as the number and scale of the input references grow.