MBMA
A Mapping Based Microbiome Analysis tool for species and resistance genes quantification
About
A main challenge in the field of metagenomics is to quickly and precisely determine the composition and the relative abundance of constituents of a microbial community. State-of-the-art metagenomic methods rely on mapping-, kmer- or assembly- based approaches for identification and quantification. However, currently available methods are either time-consuming, less sensitive and generates false positives, which leads to a lack of accuracy in quantification at gene and strain levels.
To overcome these limitations, we developed Mapping Based Microbiome Analysis (MBMA), a mapping-based approach for identification and quantification of species, strains and resistance genes, with three main innovations, the use of :
- a efficient and discriminatory database for rapid quantification,
- an advanced counting method to decrease the false discovery rate,
- combined with variant calling from samples sequences for an accurate abundance prediction.
MBMA identifies and quantifies constituents (species, resistance genes) from metagenomic samples by mapping reads against a database and performing variant calling. Other constituents can be quantifies by changing the database. It has 3 way of working :
- mapping, it simply map reads against an indexed reference database, using different mapping tools (bowtie2, bwa and novoalign) and different counting methods (best, ex-aequo and shared), for non redundant databases.
- variant, it performs, in addition to the mapping step, a variant calling step. Reads are mapped against a clustered database, and then variant calling using GATK is performed, to able an accurate quantification at a gene level.
- mode, it provide two presets modes for the identification of species (option : --species) and resistance genes (option : --resistance). For bacterial species, reads are mapped reads against RefMG.v1, and for resistance genes, against ResFinder.
Version
1.0