CAMAMED: a pipeline for composition-aware mapping-based analysis of metagenomic data.

ABSTRACT: Metagenomics is the study of genomic DNA recovered from a microbial community. Both assembly-based and mapping-based methods have been used to analyze metagenomic data. When appropriate gene catalogs are available, mapping-based methods are preferred over assembly based approaches, especially for analyzing the data at the functional level. In this study, we introduce CAMAMED as a composition-aware mapping-based metagenomic data analysis pipeline. This pipeline can analyze metagenomic samples at both taxonomic and functional profiling levels. Using this pipeline, metagenome sequences can be mapped to non-redundant gene catalogs and the gene frequency in the samples are obtained. Due to the highly compositional nature of metagenomic data, the cumulative sum-scaling method is used at both tax

SUBMITTER: Norouzi-Beirami MH 

PROVIDER: S-EPMC7787360 | biostudies-literature | 2021 Mar

REPOSITORIES: biostudies-literature