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.

Prevalence of Antibiotic Resistance Genes among Human Gut-Derived Bifidobacteria

“…The bifidobacterial strains used in this study were screened for genomic islands, evaluating the genes flanking the predicted AR genes in the range of 10 kb, using homology searches (46) and the software COLOMBO (21). Putative mobile elements such as episomes, conjugative transposons, and prophages were predicted through homology searches against in-house-generated databases (http://probiogenomics.unipr.it/sw/MobElemDB.zip), including genes retrieved from the National Center for Biotechnology Information (NCBI) database.…”

Phage Biodiversity in Artisanal Cheese Wheys Reflects the Complexity of the Fermentation Process

“…Protein-encoding open reading frames (ORFs) were predicted using a combination of the methods Prodigal v2.6 [33] and BLASTX [34] followed by manual assessment, curation, and correction of the predicted open reading frames. A functional annotation of ORFs was performed on the basis of BLASTP [35] analysis against the non-redundant protein database (nr) provided by the National Centre for Biotechnology Information (located at: ) as well as using the MEGAnnotator pipeline [36]. The proposed functions of many ORFs were further validated by querying protein domain databases Pfam [37], the National Center for Biotechnology Information (NCBI) Conserved Domain Database [38], and by performing homology prediction searches using HHPred [39].…”

Genome Sequence of Serratia marcescens Phage BF

“…Illumina MiSeq sequencing (mean coverage depth of 21.55-fold) was performed, followed by genome assembly using MIRA version 4.0.2 through the MEGAnnotator pipeline (4). Quality of the final contig was improved using the Burrows-Wheeler aligner, the SAMtools suite, and VarScan version 2.2.3.…”