MetaSanity: an integrated microbial genome evaluation and annotation pipeline.

Christopher J Neely,Elaina D Graham,Benjamin J Tully,Alfonso Valencia

doi:10.1093/bioinformatics/btaa512

Abstract

SummaryAs the importance of microbiome research continues to become more prevalent and essential to understanding a wide variety of ecosystems (e.g. marine, built, host associated, etc.), there is a need for researchers to be able to perform highly reproducible and quality analysis of microbial genomes. MetaSanity incorporates analyses from 11 existing and widely used genome evaluation and annotation suites into a single, distributable workflow, thereby decreasing the workload of microbiologists by allowing for a flexible, expansive data analysis pipeline. MetaSanity has been designed to provide separate, reproducible workflows that (i) can determine the overall quality of a microbial genome, while providing a putative phylogenetic assignment, and (ii) can assign structural and functional gene annotations with varying degrees of specificity to suit the needs of the researcher. The software suite combines the results from several tools to provide broad insights into overall metabolic function. Importantly, this software provides built-in optimization for ‘big data’ analysis by storing all relevant outputs in an SQL database, allowing users to query all the results for the elements that will most impact their research.Availability and implementationMetaSanity is provided under the GNU General Public License v.3.0 and is available for download at https://github.com/cjneely10/MetaSanity. This application is distributed as a Docker image. MetaSanity is implemented in Python3/Cython and C++. Instructions for its installation and use are available within the GitHub wiki page at https://github.com/cjneely10/MetaSanity/wiki, and additional instructions are available at https://cjneely10.github.io/year-archive/. MetaSanity is optimized for users with limited programing experience.Supplementary information Supplementary data are available at Bioinformatics online.

Highlights

The analysis of microbial genomes has become an increasingly common task for many fields of biology and geochemistry
MetaSanity provides genome quality evaluation, phylogenetic assignment, as well as structural and functional annotation through a variety of integrated programs based on the procedure described in ref
While each component contained within the two pipelines runs independently and generates component specific outputs, MetaSanity combines all outputs into a single queryable SQL database that allows fast and easy retrieval of data – in this case, gene annotations and other related genomic data

Summary

As the importance of microbiome research continues to become more prevalent and essential to understanding a wide variety of ecosystems (e.g., marine, built, host-associated, etc.), there is a need for researchers to be able to perform highly reproducible and quality analysis of microbial genomes. MetaSanity has been designed to provide separate, reproducible workflows, that (1) can determine the overall quality of a microbial genome, while providing a putative phylogenetic assignment, and (2) can assign structural and functional gene annotations with varying degrees of specificity to suit the needs of the researcher. The software suite combines the results from several tools to provide broad insights into overall metabolic function and putative extracellular localization of peptidases and carbohydrate-active enzymes. This software provides built-in optimization for “big data” analysis by storing all relevant outputs in an SQL database, allowing users to query all the results for the elements that will most impact their research.

Introduction

PhyloSanity

FuncSanity

BioMetaDB

Results