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PATRIC, the PAThosystems Resource Integration Center, is the NIH/NIAID-funded
Bacterial Bioinformatics Resource Center, a web-based resource providing integrated omics
data and analysis tools to support biomedical research on bacterial infectious diseases
and antimicrobial resistance.
At PATRIC, users can upload their private data into a workspace, analyze
it using high-throughput services, compare it with other public data using visual
analytics tools, and share results with other users.
Oct 04, 2019 | New Bioinformatics Hub at UChicago Enables Next-Gen Infectious Disease Research read more →
July 31, 2019 | This PATRIC release includes a new Fastq Utilities Service and over 24,500 new microbial genomes.
March 5, 2019 | In this release, PATRIC has added 18,250 new genomes with AMR panel data added since January release.
Feb 1, 2019 | This PATRIC release includes over 9,200 new genomes bringing the total to over 215,000.
In addition to the current Tutorials, User Guides, and Webinars, PATRIC now features YouTube videos.
Browse all posts →
The Genome Assembly Service allows single or multiple assemblers to be invoked to assemble reads and compare results.
The Genome Annotation Service uses the Rapid Annotation using Subsystem Technology tool kit (RASTtk) to provide annotation of genomic features and associated functions.
The Comprehensive Genome Analysis Meta-Service accepts raw reads and performs assembly, annotation, subsystem summary, and comparative analysis with similar genomes in PATRIC.
The PATRIC BLAST service integrates the BLAST (Basic Local Alignment Search Tool) algorithms to perform searches against public or private genomes in PATRIC.
The Similar Genome Finder Service finds and returns similar public genomes in PATRIC via genome distance estimation using the Mash/MinHash algorithm.
The Variation Analysis Service can be used to identify and annotate sequence variations against a reference genome including SNPs, MNPs, insertions, and deletions.
The Tn-Seq Analysis Service facilitates determination of essential and conditionally essential regions in bacterial genomes from Tn-Seq experiment data.
The Phylogenetic Tree Building Service enables construction of custom codon-based phylogenetic trees for user-selected genomes using RAxML with single copy protein families.
The Whole Genome Alignment Service aligns user-selected genomes using progressiveMauve and presents the results in an interactive viewer. Up to 20 genomes can be aligned.
The Metagenomic Read Mapping Service uses k-mer alignment (KMA) to align reads against antibiotic resistance genes from CARD and virulence factors from VFDB.
The Taxonomic Classification Service uses Kraken 2 to compute taxonomic classification for read data from metagenomic samples, providing initial profile of constituents.
The Metagenomic Binning Service bins read or contig data into a set of genomes, allowing reconstruction of bacterial and archaeal genomes from environmental samples.
The Differential Expression Import Service uploads user-provided, pre-processed differential expression data to the user's private workspace for further analysis.
The RNA-Seq Analysis Service aligns, assembles, and tests differential expression on RNA-Seq data, using Tuxedo for bacterial data and HISAT2 for host (human) data.
The Protein Family Sorter tool displays the distribution of specific protein families across a set of user-selected genomes in an interactive heatmap.
The Proteome Comparison Service performs protein sequence-based genome comparison using bidirectional BLASTP for user-selected genomes and a reference genome.
The Comparative Pathway Service allows users to identify a set of pathways based on taxonomy, EC number, pathway ID, pathway name and/or specific annotation type.
The Model Reconstruction Service integrates multiple technologies to generate draft genome-scale metabolic models starting with an assembled genome sequence.
The ID Mapper tool maps PATRIC identifiers to those from other prominent external databases such as GenBank, RefSeq, EMBL, UniProt, KEGG, etc., and vice versa.
The Fastq Utilities Service provides capability for aligning, measuring base call quality, and trimming fastq read files. Each of the operations are configurable.