MetaSanity: An integrated, customizable microbial genome evaluation and annotation pipeline

Abstract

11Summary 12 As the importance of microbiome research continues to become more prevalent and essential to 13 understanding a wide variety of ecosystems (e.g., marine, built, host-associated, etc.), there is a 14 need for researchers to be able to perform highly reproducible and quality analysis of microbial 15 genomes. MetaSanity incorporates analyses from eleven existing and widely used genome 16 evaluation and annotation suites into a single, distributable workflow, thereby decreasing the 17 workload of microbiologists by allowing for a flexible, expansive data analysis pipeline. 18 MetaSanity has been designed to provide separate, reproducible workflows, that (1) can 19 determine the overall quality of a microbial genome, while providing a putative phylogenetic 20 assignment, and (2) can assign structural and functional gene annotations with varying degrees of 21 specificity to suit the needs of the researcher. The software suite combines the results from 22 several tools to provide broad insights into overall metabolic function and putative extracellular 23 localization of peptidases and carbohydrate-active enzymes. Importantly, this software provides 24 built-in optimization for "big data" analysis by storing all relevant outputs in an SQL database, 25 allowing users to query all the results for the elements that will most impact their research. 26 Availability and implementation 27 MetaSanity is provided under the GNU General Public License v.3.0 and is available for 28 download at https://github.com/cjneely10/MetaSanity. This application is distributed as a Docker 29 image. MetaSanity is implemented in Python3/Cython and C++.

Time-series transcriptomics from cold, oxic subseafloor crustal fluids reveals a motile, mixotrophic microbial community

“…Tree formatting was performed using the Interactive Tree of Life [42]. Functional orthologies as defined by the KEGG database [43] were annotated using MetaSanity v1.2.0 [44] (Supplementary Methods). Genes related to iron acquisition, storage, and oxidation/reduction were annotated using the FeGenie tool [45].…”

Marine Dadabacteria exhibit genome streamlining and phototrophy-driven niche partitioning

“…MAGs were assessed for putative metabolic functionality through the FuncSanity 105 workflow of the tool MetaSanity(Neely et al, 2019). All downstream analysis uses the of 106 putative CDS as predicted by Prokka (v1.13.3)(Seemann, 2014).…”

Time-series transcriptomics from cold, oxic subseafloor crustal fluids reveals a motile, mixotrophic microbial community

“…Tree formatting was performed using the Interactive Tree of Life [42]. Functional orthologies as defined by the KEGG database [43] were annotated using MetaSanity [44] (Supplemental Methods). Genes related to iron acquisition, storage, and oxidation/reduction were annotated using the FeGenie tool [45].…”