Abstracts

Oral Presentation Abstracts
utility of Salmonella serotyping when integrated
into a platform of WGS-based pathogen
subtyping and characterization.
n S4:5
PATRIC PIPELINE
F. Xia 1 , T. Brettin 2 , S. Boisvert 2 , N. R. Conrad 2 ,
J. J. Davis 1 , T. Disz 1 , J. Edirisinghe 2 , R. A. Edwards
3 , C. Henry 1 , R. W. Kenyon 4 , D. Machi 4 ,
C. Mao 4 , G. J. Olsen 5 , R. Olson 2 , R. Overbeek 6 ,
B. Parrello 6 , G. D. Pusch 6 , M. P. Shukla 2 , B. W.
Sobral 4 , R. L. Stevens 1 , V. Vonstein 6 , A. Warren
4 , R. Will 4 , H. Yoo 4 , A. R. Wattam 4 ;
1
University of Chicago, Chicago, IL, 2 Argonne
National Laboratory, Lemont, IL, 3 San Diego
State University, San Diego, CA, 4 Virginia
Tech, Blacksburg, VA, 5 University of Illinois
at Urbana and Champaign, Urbana, IL, 6 Fellowship
for Interpretation of Genomes, Burr
Ridge, IL.
Recent advances in DNA sequencing technology
accompanied by plummeting per-base cost
is making sequence-based applications more
amenable. While a plethora of bioinformatics
databases and workflows exist, their capabilities
are often hampered by the inconsistent
use of analysis tools. PATRIC, the NIAIDfunded
comprehensive bacterial bioinformatics
resource, has integrated more than 30,000
consistently annotated prokaryote genomes
with a focus on human pathogenic species.
Here we present PATRIC’s new computational
services that support the assembly, annotation
and metabolic modeling of user-supplied
genomes in the same consistent fashion. These
services, integrated with PATRIC’s collections
of specialty genes such as antibiotic resistance
determinants and virulence factors, will enable
users to rapidly process newly sequenced
pathogens and investigate key pathogenic
determinants in foodborne outbreaks using the
powerful visualization and comparative analysis
tools in PATRIC. We have implemented
the new services with three principles in mind.
(1) Controlled vocabulary. At the heart of
PATRIC’s annotation service is a controlled
vocabulary for functional annotation derived
from the curated subsystems and protein families
in the RAST and SEED systems [2]. Similarly,
the new model reconstruction service
relies on our curated biochemistry data [5].
These curation efforts ensure newly sequenced
genomes can be automatically annotated and
modeled and readily compared with existing
reference data. (2) Modular design. In genome
assembly as well as other bioinformatic analyses,
there is often no single tool best suited
for all occasions [4]. We have added support
for more than 30 tools for error correction,
contig assembly, scaffolding, contig evaluation,
consensus building, gene calling, overlap
removal, as well as many custom algorithms
[3]. These modules are condensed into a few
curated workflows to ensure convenient and
efficient execution as well as consistent quality
control. (3) Integrated analysis. The new
workspace allows users to upload their own
data for analysis, and upon completion the
private results are immediately integrated into
PATRIC. This enables users to take advantage
of PATRIC’s data (drug targets, omics, AMR
and other clinical metadata) and comparative
tools (protein family sorter, phylogeny, heat
maps, etc). In addition to these services, we
are actively building support for batch analysis
and SNP-level comparative analysis for closely
related genomes. URL: https://www.patricbrc.
org. References: [1] Gillespie, et al. “PATRIC:
... (2011). [2] Overbeek, et al. “The SEED
... (RAST).” Nucleic acids research (2014):
D206-D214. [3] Brettin, et al. “RASTtk ...”
Scientific reports 5 (2015). [4] Earl, et al. “Assemblathon
...” Genome research (2011). [5]
Henry, et al. “High-throughput ... models.”
Nature biotechnology (2010).
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