Faucon, P. | Search bioRxiv

bioRxiv2024

Inosculation As A Tool For Living Architecture: Methods And Early Results

Among the ways to introduce more plants within the city, living architecture could lower material required for building a house. However, trees are not supposed to have a house-like shape, so it is needed to give them this shape. That is why, we choose to investigate the assembly of living trees through inosculation. To do so, we initiated this work in March 2021, in our greenhouse, on five species: Acer platanoides, Celtis australis, Cornus Mas, Corylus colurna and Pyrus communis. We tested two types of contact (parallel or perpendicular) between two trees from the same species with scraped bark, or not, maintained by diverse tools (screw, fishing line, buddy tape and flexible stretch tie). From this, we get interesting anastomosis results with half of the trees showing signs of inosculation by spring 2022.

plant biology↗

bioRxiv2017

SNaReSim: Synthetic Nanopore Read Simulator

Nanopores represent the first commercial technology in decades to present a significantly different technique for DNA sequencing, and one of the first technologies to propose direct RNA sequencing. Despite significant differences with previous sequencing technologies, read simulators to date make similar assumptions with respect to error profiles and their analysis. This is a great disservice to both nanopore sequencing and to computer scientists who seek to optimize their tools for the platform. Previous works have discussed the occurrence of some k-mer bias, but this discussion has been focused on homopolymers, leaving unanswered the question of whether k-mer bias exists over general k-mers, how it occurs, and what can be done to reduce the effects. In this work, we demonstrate that current read simulators fail to accurately represent k-mer error distributions, We explore the sources of k-mer bias in nanopore basecalls, and we present a model for predicting k-mers that are difficult to identify. We also propose a new SNaReSim, a new state-of-the-art simulator, and demonstrate that it provides higher accuracy with respect to 6-mer accuracy biases.

bioinformatics↗