control checks on raw sequence data coming from highthroughput sequencing pipelines and enables rapid quality control
by indicating problems that could impact downstream analyses.
The aligning function aligns reads to a reference genome sequence
using Bowtie2 [39], saving unmapped reads, and generating SamStat [109] reports of the number and quality of alignments.
5.1.2 Taxonomic
Classification
The Taxonomic Classification service can be used to identify the
microbial composition of metagenomic samples and identify potential contamination in a sample. Researchers can submit their reads
(paired or single-end long or short, zipped or unzipped), Sequence
Read Archive accession numbers, or contigs to this service. The
algorithm used for Taxonomic Classification is Kraken2 [38],
which uses exact alignment of k-mers for classification accuracy.
Job output includes the standard Kraken report format, with each
bacterial taxon hyperlinked to the matching page in PATRIC. The
service also returns a Krona plot [110] that shows the percentage of
reads that mapped to each taxon and allows the user to explore
selected taxa.
5.1.3 Metagenomic Read
Mapping
Researchers studying antimicrobial resistance or virulence may be
interested in analyzing genes in mixed or metagenomic read sets or
in quickly determining if these genes are present in a sequence. The
Metagenomic Read Mapping Service enables researchers to see if
reads that map to these specific genes are present in their sequence.
It uses KMA [111], which uses k-mer seeding and the Needleman–
Wunsch algorithm to accurately align the reads to genes of interest,
with reference gene sets from the Comprehensive Antibiotic Resistance Database (CARD) [112] and the Virulence Factor Database
(VFDB) [113] being the two options that PATRIC currently provides. The service returns HTML and text versions of the standard
KMA report, which shows detailed mapping information, links to
genes in PATRIC with high similarity, and a consensus sequence
assembled from the aligned reads.
5.1.4 Assembly
More than 37,000 genome assembly jobs have been submitted
since PATRIC started this service on January 1, 2015. In addition
to the standard SPAdes [44] assembler, the service was recently
expanded to include metaSPAdes [114] for metagenomic reads,
plasmidSPAdes [115] for assembling plasmids, Canu [50] for longread assembly, and Unicycler [48] for hybrid long- and short-read
assemblies. The SPAdes recipe for assembling the reads from single
cells is also an option that can be selected. Assemblies can be
polished using either Racon, [53] and Pilon [116] can be selected
to polish long- and short-read assemblies, respectively. Read
mapping is performed to generate accurate coverage statistics
Mycobacterial ID and Characterization Using WGS
435
by indicating problems that could impact downstream analyses.
The aligning function aligns reads to a reference genome sequence
using Bowtie2 [39], saving unmapped reads, and generating SamStat [109] reports of the number and quality of alignments.
5.1.2 Taxonomic
Classification
The Taxonomic Classification service can be used to identify the
microbial composition of metagenomic samples and identify potential contamination in a sample. Researchers can submit their reads
(paired or single-end long or short, zipped or unzipped), Sequence
Read Archive accession numbers, or contigs to this service. The
algorithm used for Taxonomic Classification is Kraken2 [38],
which uses exact alignment of k-mers for classification accuracy.
Job output includes the standard Kraken report format, with each
bacterial taxon hyperlinked to the matching page in PATRIC. The
service also returns a Krona plot [110] that shows the percentage of
reads that mapped to each taxon and allows the user to explore
selected taxa.
5.1.3 Metagenomic Read
Mapping
Researchers studying antimicrobial resistance or virulence may be
interested in analyzing genes in mixed or metagenomic read sets or
in quickly determining if these genes are present in a sequence. The
Metagenomic Read Mapping Service enables researchers to see if
reads that map to these specific genes are present in their sequence.
It uses KMA [111], which uses k-mer seeding and the Needleman–
Wunsch algorithm to accurately align the reads to genes of interest,
with reference gene sets from the Comprehensive Antibiotic Resistance Database (CARD) [112] and the Virulence Factor Database
(VFDB) [113] being the two options that PATRIC currently provides. The service returns HTML and text versions of the standard
KMA report, which shows detailed mapping information, links to
genes in PATRIC with high similarity, and a consensus sequence
assembled from the aligned reads.
5.1.4 Assembly
More than 37,000 genome assembly jobs have been submitted
since PATRIC started this service on January 1, 2015. In addition
to the standard SPAdes [44] assembler, the service was recently
expanded to include metaSPAdes [114] for metagenomic reads,
plasmidSPAdes [115] for assembling plasmids, Canu [50] for longread assembly, and Unicycler [48] for hybrid long- and short-read
assemblies. The SPAdes recipe for assembling the reads from single
cells is also an option that can be selected. Assemblies can be
polished using either Racon, [53] and Pilon [116] can be selected
to polish long- and short-read assemblies, respectively. Read
mapping is performed to generate accurate coverage statistics
Mycobacterial ID and Characterization Using WGS
435