using Bowtie2 [39], Minimap2 [117], and SAMtools [59]. The
service returns an assembly graph using Bandage [118] and a
contig file.
5.1.5 Annotation
More than 178,000 annotation jobs have been submitted to
PATRIC since this service was launched in January 2015, making
it the most highly used and popular service by far. It uses the RAST
tool kit (RASTtk) [119] to provide annotation of genomic features
to bacterial, archaeal, and most recently bacteriophage genomes
[120]. Each annotation job also includes quality statistics based on
CheckM [121] and an internal RAST model that assesses quality
based on the occurrence and completeness of subsystem roles in the
genome [122, 123]. Genus-specific (PLFam) or global (PGFam)
protein families [124] are assigned for each gene, unless it is a
singleton that lacks a homolog across the proteins currently in the
database. Once annotated, a submitted genome is deposited in an
assigned workspace that the researcher has private access to and is
available for comparison with any other genome or group of genomes in the database.
PATRIC actively curates both AMR protein annotations and
laboratory-derived AMR phenotype data associated with public
genomes [125, 126], and so the annotation system can accurately
project over 600 hand-curated AMR protein functions. To provide
an additional means of comparison, the annotation system also
searches for genes with high similarity to those curated by the
CARD [112] and NCBI AMR gene database projects [127]. A
similar search is conducted for genes with high similarity based on
virulence factors from VFDB [113], Victors [128], and the special
PATRIC virulence factor database [129].
5.1.6 Comprehensive
Genome Analysis
PATRIC originally provided researchers with the ability to assemble
and annotate their genomes using two distinct services. In the
Spring of 2018, the Comprehensive Genome Analysis Service was
launched to provide a streamlined analysis “meta-service” that
accepts raw genome reads and performs a comprehensive analysis
including assembly, annotation, identification of nearest neighbors,
and a basic comparative analysis that includes a subsystem summary,
phylogenetic tree, and the features that distinguish the genome
from its nearest neighbors. The output includes a genome quality
assessment, AMR gene and phenotype predictions, specialty genes,
subsystem overview, identification of the closest genome
sequences, a phylogenetic tree, and a list of features that distinguish
the genome from its nearest neighbors. The Comprehensive
Genome Analysis Service has quickly risen to be one of the most
popular services in PATRIC with over 15,000 jobs being completed since its launch in April 2018.
436
Marco A. Riojas et al.
service returns an assembly graph using Bandage [118] and a
contig file.
5.1.5 Annotation
More than 178,000 annotation jobs have been submitted to
PATRIC since this service was launched in January 2015, making
it the most highly used and popular service by far. It uses the RAST
tool kit (RASTtk) [119] to provide annotation of genomic features
to bacterial, archaeal, and most recently bacteriophage genomes
[120]. Each annotation job also includes quality statistics based on
CheckM [121] and an internal RAST model that assesses quality
based on the occurrence and completeness of subsystem roles in the
genome [122, 123]. Genus-specific (PLFam) or global (PGFam)
protein families [124] are assigned for each gene, unless it is a
singleton that lacks a homolog across the proteins currently in the
database. Once annotated, a submitted genome is deposited in an
assigned workspace that the researcher has private access to and is
available for comparison with any other genome or group of genomes in the database.
PATRIC actively curates both AMR protein annotations and
laboratory-derived AMR phenotype data associated with public
genomes [125, 126], and so the annotation system can accurately
project over 600 hand-curated AMR protein functions. To provide
an additional means of comparison, the annotation system also
searches for genes with high similarity to those curated by the
CARD [112] and NCBI AMR gene database projects [127]. A
similar search is conducted for genes with high similarity based on
virulence factors from VFDB [113], Victors [128], and the special
PATRIC virulence factor database [129].
5.1.6 Comprehensive
Genome Analysis
PATRIC originally provided researchers with the ability to assemble
and annotate their genomes using two distinct services. In the
Spring of 2018, the Comprehensive Genome Analysis Service was
launched to provide a streamlined analysis “meta-service” that
accepts raw genome reads and performs a comprehensive analysis
including assembly, annotation, identification of nearest neighbors,
and a basic comparative analysis that includes a subsystem summary,
phylogenetic tree, and the features that distinguish the genome
from its nearest neighbors. The output includes a genome quality
assessment, AMR gene and phenotype predictions, specialty genes,
subsystem overview, identification of the closest genome
sequences, a phylogenetic tree, and a list of features that distinguish
the genome from its nearest neighbors. The Comprehensive
Genome Analysis Service has quickly risen to be one of the most
popular services in PATRIC with over 15,000 jobs being completed since its launch in April 2018.
436
Marco A. Riojas et al.