PlasGUN: gene prediction in plasmid metagenomic short reads using deep learning.

Abstract

SummaryWe present the first tool of gene prediction, PlasGUN, for plasmid metagenomic short-read data. The tool, developed based on deep learning algorithm of multiple input Convolutional Neural Network, demonstrates much better performance when tested on a benchmark dataset of artificial short reads and presents more reliable results for real plasmid metagenomic data than traditional gene prediction tools designed primarily for chromosome-derived short reads.Availability and implementationThe PlasGUN software is available at http://cqb.pku.edu.cn/ZhuLab/PlasGUN/ or https://github.com/zhenchengfang/PlasGUN/.Supplementary information Supplementary data are available at Bioinformatics online.