DeepMicrobes

DeepMicrobes: taxonomic classification for metagenomics with deep learning
Supplementary data for the paper is available at https://github.com/MicrobeLab/DeepMicrobes-data
IMPORTANT: The new DeepMicrobes (beta version) is available now. Please feel free to contact us if you have any suggestions or encounter any errors.

Usage

• How to install
• How to convert fastq/fasta sequences to TFRecord
• How to make predictions on a metagenome dataset
• How to generate taxonomic profiles
• How to choose the confidence threshold
• How to train the DNN model of DeepMicrobes
• How to submit to GPUs
• Suggestions on training a custom model (for advanced users)

Contact

Any issues with the DeepMicrobes framework can be filed with GitHub issue tracker. We are committed to maintain this repository to assist users and tackle errors.

Email

• liangqx7@mail2.sysu.edu.cn (Qiaoxing Liang)

Citation

Qiaoxing Liang, Paul W Bible, Yu Liu, Bin Zou, Lai Wei, DeepMicrobes: taxonomic classification for metagenomics with deep learning, NAR Genomics and Bioinformatics, Volume 2, Issue 1, March 2020, lqaa009, https://doi.org/10.1093/nargab/lqaa009