SUMMARY: We present MetaMarker, a pipeline for discovering metagenomic biomarkers from WMS 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 WMS 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 colorectal cancer 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.