PATRIC March 2019 Data and Website Release

Published on 2019-04-05

This PATRIC release includes a new Metagenome Taxonomic Classification Service; a new Metagenomic Read Mapping Service; a new Codon Tree option for the Phylogenetic Tree Building Service; and over 18,250 new microbial genomes.

Data Updates:

New Genomes

In this release, PATRIC has added 18,250 new genomes with AMR panel data added since January release, which includes 10,000 genomes from MTB Cryptic consortium and 5000 genomes from SRA with antibiogram data. All of these genomes were assembled from reads in SRA. We also updated MLST reference database and MLST assignments for all public genomes and standardized host names for all public genomes to support development of new machine learning models to predict host specificity. The total number of genomes and plasmids in PATRIC is now over 230,000. The full list of available microbial and host genomes can be accessed here.

New Website Features:

The new Metagenome Taxonomic Classification Service accepts reads or contigs from sequencing of a metagenomic sample and uses Kraken 2 to assign the reads to taxonomic bins, providing an initial profile of the possible constituent organisms present in the sample. The Taxonomic Classification Service is available from the Services top menu.

The new Metagenomic Read Mapping Service uses KMA to align reads against antibiotic resistance genes and virulence factors in PATRIC. The Metagenomic Read Mapping Service is available from the Services top menu.

The Phylogenetic Tree Builiding Service now includes a faster Codon Tree option that utilizes PATRIC PGFams as homology groups and analyzes aligned proteins and coding DNA from single-copy genes using the program RAxML. Up to 100 genomes can be analyzed. The Phylogenetic Tree Building Service is available from the Services top menu.