Biology subjects

Van der Jeugt, F.

Publications and source records attributed to Van der Jeugt, F..

2 recordsLinked to original sources

bioRxiv2021

FragGeneScanRs: better and faster gene prediction for short reads

FragGeneScanRs is a better and faster Rust implementation of the FragGeneScan gene prediction model for short and error-prone reads. Its command line interface is backward compatible and adds extra features for more flexible usage. Compared to the original C implementation, shotgun metagenomic reads are processed up to 22 times faster using a single thread, with better scaling for multithreaded execution. Availability and implementationThe Rust code of FragGeneScanRs is freely available from GitHub under the GPL-3.0 license, with instructions for installation, usage and other documentation.

bioinformatics↗

bioRxiv2021

UMGAP: the Unipept MetaGenomics Analysis Pipeline

Shotgun metagenomics is now commonplace to gain insights into communities from diverse environments, but fast, memory-friendly, and accurate tools are needed for deep taxonomic analysis of the metagenome data. To meet this need we developed UMGAP, a highly versatile open source command line tool implemented in Rust for taxonomic profiling of shotgun metagenomes. It differs from state-of-the-art tools in its use of protein code regions identified in short reads for robust taxonomic identifications, a broad-spectrum index that can identify both archaea, bacteria, eukaryotes and viruses, a non-monolithic design, and support for interactive visualizations of complex biodiversities.

bioinformatics↗