Skip to main page content
Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2019 Oct 1;35(19):3812-3814.
doi: 10.1093/bioinformatics/btz123.

MetaMarker: A Pipeline for De Novo Discovery of Novel Metagenomic Biomarkers

Affiliations
Free PMC article

MetaMarker: A Pipeline for De Novo Discovery of Novel Metagenomic Biomarkers

Mohamad Koohi-Moghadam et al. Bioinformatics. .
Free PMC article

Abstract

Summary: We present MetaMarker, a pipeline for discovering metagenomic biomarkers from whole-metagenome sequencing samples. Different from existing methods, MetaMarker is based on a de novo approach that does not require mapping raw reads to a reference database. We applied MetaMarker on whole-metagenome sequencing of colorectal cancer (CRC) stool samples from France to discover CRC specific metagenomic biomarkers. We showed robustness of the discovered biomarkers by validating in independent samples from Hong Kong, Austria, Germany and Denmark. We further demonstrated these biomarkers could be used to build a machine learning classifier for CRC prediction.

Availability and implementation: MetaMarker is freely available at https://bitbucket.org/mkoohim/metamarker under GPLv3 license.

Supplementary information: Supplementary data are available at Bioinformatics online.

Similar articles

See all similar articles

LinkOut - more resources

Feedback