DATMA: Distributed AuTomatic Metagenomic Assembly and annotation framework

• Published in: PeerJ (San Francisco, CA) Vol. 8; p. e9762
• Main Authors: Benavides, Andres, Sanchez, Friman, Alzate, Juan F, Cabarcas, Felipe
• Format: Journal Article
• Language: English
• Published: United States PeerJ. Ltd 03-09-2020; PeerJ, Inc; PeerJ Inc
• Subjects: Algorithm; Analysis; Bioinformatics; Computational Biology; Datasets; Distributed and Parallel Computing; Distributed computing; DNA sequencing; Genes; Genomes; Genomics; Graph representations; Grid computing; Management reports; Metagenomics; Nucleotide sequence; Quality control; RNA; rRNA 16S; Software; Taxonomy; Workflow; Metagenomics; Grid computing; Workflow; Algorithm; Bioinformatics; Distributed computing
• ISSN: 2167-8359; 2167-8359
• DOI: 10.7717/peerj.9762

A prime objective in metagenomics is to classify DNA sequence fragments into taxonomic units. It usually requires several stages: read's quality control, de novo assembly, contig annotation, gene prediction, etc. These stages need very efficient programs because of the number of reads from the projects. Furthermore, the complexity of metagenomes requires efficient and automatic tools that orchestrate the different stages.
DATMA is a pipeline for fast metagenomic analysis that orchestrates the following: sequencing quality control, 16S rRNA-identification, reads binning, de novo assembly and evaluation, gene prediction, and taxonomic annotation. Its distributed computing model can use multiple computing resources to reduce the analysis time.
We used a controlled experiment to show DATMA functionality. Two pre-annotated metagenomes to compare its accuracy and speed against other metagenomic frameworks. Then, with DATMA we recovered a draft genome of a novel Anaerolineaceae from a biosolid metagenome.
DATMA is a bioinformatics tool that automatically analyzes complex metagenomes. It is faster than similar tools and, in some cases, it can extract genomes that the other tools do not. DATMA is freely available at https://github.com/andvides/DATMA.