Deep learning approach to metagenomic binning

Understanding the diversity and abundance of microbial populations is paramount to the health of humans and the environment. Estimating the diversity of these populations from whole metagenome shotgun (WMS) sequencing reads is difficult because the size of these datasets and overlapping reads limit what kinds of analysis we can do. Current methods require matching reads to a database of known microbes. These methods are either too slow or lack the sensitivity needed to identify novel species. We propose a convolutional neural network (CNN) based approach to metagenomic binning that embeds reads into a low-dimensional vector space based on taxonomic classification. We show that our method can get the speed and sensitivity necessary taxonomic classification. Our method was able to achieve 13% accuracy on identifying novel genus of bacteria as compared to 7% accuracy of k-mer embedding. At the same time, the speed of our method is within an order of magnitude of that of k-mer embedding, making it viable as a metagenomic analysis tool.

Department dc:contributor.department

Massachusetts Institute of Technology. Department of Electrical Engineering and Computer Science.

Grantor dc:publisher

Massachusetts Institute of Technology

Year dc:date.issued

2018

Author dc:creator

• Chung, Ryan Kyong-doc

Advisor dc:contributor.advisor

• Bonnie Berger.

• Electrical Engineering and Computer Science.

Statement dc:rights

• MIT theses are protected by copyright. They may be viewed, downloaded, or printed from this source but further reproduction or distribution in any format is prohibited without written permission.

Licence dc:rights.uri

• http://dspace.mit.edu/handle/1721.1/7582

Language dc:language.iso

eng

Handle dc:identifier.uri

http://hdl.handle.net/1721.1/119755

OAI identifier oai:identifier

oai:dspace.mit.edu:1721.1/119755