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Posts
MetaSanity - Output
Published:
In a previous post, we walked through several examples of using BioMetaDB - a Bio-focused command-line SQL wrapper package - to query the results of our MetaSanity pipeline runs. The contents of each project is self-contained, making it very easy for users to focus their attention on getting specific information. Read more
MetaSanity v1.1 - Adding additional analyses
Published:
MetaSanity v1.1 releases 10/18/2019 with some new features! See the changelog for a complete list of changes in version 1.1. Read more
MetaSanity Demo - BioMetaDB
Published:
In this blog, we will continue our work from the previous demo blog. We had just completed both steps of the MetaSanity package, and we now have an output directory filled with output from each program and parsed tab-delimited data files (TSVs). Read more
MetaSanity Demo - Running FuncSanity
Published:
In this blog, we will continue our work from the first demo blog. Previously, we had evaluated a set of metagenomic assembled genomes (MAGs) for completion and contamination. We then queried our dataset for high quality, non-redundant genomes, and stored these to a separate directory. Read more
MetaSanity Demo - Running PhyloSanity
Published:
MetaSanity is a designed for easy generation of dynamic data analysis pipelines. The heart of the software is a queryable SQL database that allows fast and easy retrieval of genomic metadata - in this case, gene annotations and other related genomic data. Read more
portfolio
publications
Genome Sequence of Hydrogenovibrio sp. Strain SC-1, a Chemolithoautotrophic Sulfur and Iron Oxidizer
Published in American Society for Microbiology - Microbiology Resource Announcements, 2018
Hydrogenovibrio sp. strain SC-1 was isolated from pyrrhotite… Read more
Recommended citation: C. J. Neely, C. B. Khalil, A. Cervantes, R. Diaz, A. Escobar, K. Ho, S. Hoefler, H. Smith, K. Abuyen, P. Savalia, K. H. Nealson, D. Emerson, B. J. Tully, R. A. Barco, and Jan Amend. "Genome sequence of Hydrogenovibrio sp. SC-1, a Chemolithoautotrophic, Sulfur and Iron Oxidizer." In: Genome Announcements http://genomea.asm.org/content/6/5/e01581-17. https://mra.asm.org/content/6/5/e01581-17
MetaSanity: An integrated microbial genome evaluation and annotation pipeline
Published in Oxford Academic Bioinformatics, 2020
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. Read more
Recommended citation: Christopher J Neely, Elaina D Graham, Benjamin J Tully, MetaSanity: An integrated microbial genome evaluation and annotation pipeline, Bioinformatics, , btaa512, https://doi.org/10.1093/bioinformatics/btaa512 https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btaa512/5840471