title: MEGAnnotator: a user-friendly pipeline for microbial genomes assembly and annotation.
abstract: Genome annotation is one of the key actions that must be undertaken in order to decipher the genetic blueprint of organisms. Thus, a correct and reliable annotation is essential in rendering genomic data valuable. Here, we describe a bioinformatics pipeline based on freely available software programs coordinated by a multithreaded script named MEGAnnotator (Multithreaded Enhanced prokaryotic Genome Annotator). This pipeline allows the generation of multiple annotated formats fulfilling the NCBI guidelines for assembled microbial genome submission, based on DNA shotgun sequencing reads, and minimizes manual intervention, while also reducing waiting times between software program executions and improving final quality of both assembly and annotation outputs. MEGAnnotator provides an efficient way to pre-arrange the assembly and annotation work required to process NGS genome sequence data. The script improves the final quality of microbial genome annotation by reducing ambiguous annotations. Moreover, the MEGAnnotator platform allows the user to perform a partial annotation of pre-assembled genomes and includes an option to accomplish metagenomic data set assemblies. MEGAnnotator platform will be useful for microbiologists interested in genome analyses of bacteria as well as those investigating the complexity of microbial communities that do not possess the necessary skills to prepare their own bioinformatics pipeline.
authors.affiliation: Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Parco Area delle Scienze 11A, 43124 Parma, Italy.
authors.forename: Gabriele Andrea
authors.initials: GA
authors.lastname: Lugli
authors.affiliation: Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Parco Area delle Scienze 11A, 43124 Parma, Italy.
authors.forename: Christian
authors.initials: C
authors.lastname: Milani
authors.affiliation: Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Parco Area delle Scienze 11A, 43124 Parma, Italy.
authors.forename: Leonardo
authors.initials: L
authors.lastname: Mancabelli
authors.affiliation: Department of Microbiology & Alimentary Pharmabiotic Centre, APC Microbiome Institute and School of Microbiology, National University of Ireland, Western Road, Cork, Ireland.
authors.forename: Douwe
authors.initials: D
authors.lastname: van Sinderen
authors.affiliation: Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Parco Area delle Scienze 11A, 43124 Parma, Italy marco.ventura@unipr.it.
authors.forename: Marco
authors.initials: M
authors.lastname: Ventura
mesh_terms: D001483:Base Sequence; D001644:Bifidobacterium / Q000235:genetics; D019295:Computational Biology / Q000295:instrumentation / Q000379:methods*; D030541:Databases, Genetic; D064349:Genome, Microbial; D023281:Genomics; D006801:Humans; D056186:Metagenomics / Q000379:methods; D058977:Molecular Sequence Annotation; D017422:Sequence Analysis, DNA; D012984:Software
keywords: bifidobacteria; genomics; metagenomics