nucleotides used to compute the tree. It also includes suggestions
for improving the tree by removing problematic genome sequences
to increase the gene selection and improve the strength of the tree.
5.1.10 Metagenomic
Binning
The ability to reconstruct fairly complete genomes from metagenomic samples was the first metagenomic service in PATRIC.
Launched in August 2017, the Metagenomic Binning Service
assembles reads into contigs and then attempts to separate these
contigs into bins that represent the genomes of individual species.
These bins are then fully annotated, and detailed quality statistics
are computed for each bin. The binning algorithm, which can also
use contigs from previously generated metagenomic assemblies,
starts by scanning contigs for specific marker proteins that are
almost always singly occurring in the genome. The marker-protein
similarity is used to recruit similar genomes from PATRIC, which
are then used to recruit additional contigs based on distinguishing
protein k-mers. Similar to single isolate genomes, the bins are
placed in the researcher’s workspace, allowing the full use of the
PATRIC comparative analysis and visualization tools for each bin.
5.1.11 Variation Service
The Variation Analysis Service can be used to identify and annotate
sequence variations, including SNPs, SNVs, and indels. The service
enables users to upload one or multiple short-read files and align
them with a closely related reference genome. For each sample, the
service computes the variations against the reference and presents a
detailed list of Single Nucleotide Polymorphisms (SNPs), Multiple
Nucleotide Polymorphism (MNPs), insertions, and deletions with
confidence scores and effects such as ‘synonymous mutation’ and
‘frameshift’. It includes a choice of five different aligners and two
different SNP callers. The aligners include BWA-mem and BWAmem-strict [136], Bowtie2 [39], and LAST [137], and the two
SNP callers are FreeBayes [138] and SAMtools [59]. High confidence variations are downloadable in the standard VCF (Variant
Calling Format) augmented by SNP annotation. A summary table
illustrating how the variations are shared across the samples is also
provided.
5.1.12 Proteome
Comparison
PATRIC provides a Proteome Comparison service that can be used
to compare up to nine genomes with a reference. Originally built
for the RAST website [139], the improved service adds new functionality for PATRIC. This tool colors each gene based on protein
similarity using BLASTP [140] and marks each gene as unique, a
unidirectional best hit, or a bidirectional best hit when compared to
the reference genome. Researchers can now use any public or
private genome as a reference or a comparison genome. In addition,
they can upload genomes with different annotations or specific sets
of proteins. This enables a search for homologs that is not limited to
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Marco A. Riojas et al.
for improving the tree by removing problematic genome sequences
to increase the gene selection and improve the strength of the tree.
5.1.10 Metagenomic
Binning
The ability to reconstruct fairly complete genomes from metagenomic samples was the first metagenomic service in PATRIC.
Launched in August 2017, the Metagenomic Binning Service
assembles reads into contigs and then attempts to separate these
contigs into bins that represent the genomes of individual species.
These bins are then fully annotated, and detailed quality statistics
are computed for each bin. The binning algorithm, which can also
use contigs from previously generated metagenomic assemblies,
starts by scanning contigs for specific marker proteins that are
almost always singly occurring in the genome. The marker-protein
similarity is used to recruit similar genomes from PATRIC, which
are then used to recruit additional contigs based on distinguishing
protein k-mers. Similar to single isolate genomes, the bins are
placed in the researcher’s workspace, allowing the full use of the
PATRIC comparative analysis and visualization tools for each bin.
5.1.11 Variation Service
The Variation Analysis Service can be used to identify and annotate
sequence variations, including SNPs, SNVs, and indels. The service
enables users to upload one or multiple short-read files and align
them with a closely related reference genome. For each sample, the
service computes the variations against the reference and presents a
detailed list of Single Nucleotide Polymorphisms (SNPs), Multiple
Nucleotide Polymorphism (MNPs), insertions, and deletions with
confidence scores and effects such as ‘synonymous mutation’ and
‘frameshift’. It includes a choice of five different aligners and two
different SNP callers. The aligners include BWA-mem and BWAmem-strict [136], Bowtie2 [39], and LAST [137], and the two
SNP callers are FreeBayes [138] and SAMtools [59]. High confidence variations are downloadable in the standard VCF (Variant
Calling Format) augmented by SNP annotation. A summary table
illustrating how the variations are shared across the samples is also
provided.
5.1.12 Proteome
Comparison
PATRIC provides a Proteome Comparison service that can be used
to compare up to nine genomes with a reference. Originally built
for the RAST website [139], the improved service adds new functionality for PATRIC. This tool colors each gene based on protein
similarity using BLASTP [140] and marks each gene as unique, a
unidirectional best hit, or a bidirectional best hit when compared to
the reference genome. Researchers can now use any public or
private genome as a reference or a comparison genome. In addition,
they can upload genomes with different annotations or specific sets
of proteins. This enables a search for homologs that is not limited to
438
Marco A. Riojas et al.