MetaMarker: a pipeline for de novo discovery of novel metagenomic biomarkers.
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ABSTRACT:
SUBMITTER: Koohi-Moghadam M
PROVIDER: S-EPMC6761932 | biostudies-literature | 2019 Oct
REPOSITORIES: biostudies-literature
Publications
MetaMarker: a pipeline for de novo discovery of novel metagenomic biomarkers.
Koohi-Moghadam Mohamad M Borad Mitesh J MJ Tran Nhan L NL Swanson Kristin R KR Boardman Lisa A LA Sun Hongzhe H Wang Junwen J
Bioinformatics (Oxford, England) 20191001 19
<h4>Summary</h4>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 indepen ...[more]
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