All Tools & Services


The Genome Assembly Service allows single or multiple assemblers to be invoked to compare results. The service attempts to select the best assembly.


The Genome Annotation Service provides annotation of genomic features using the RAST tool kit (RASTtk) for bacteria and VIGOR4 for viruses. The service accepts a FASTA formatted contig file and an annotation recipe based on taxonomy to provide an annotated genome.

Comparative Systems

The Comparative Systems Service allows users to identify a set of pathways, subsystems and protein families for given genome(s) or genome group(s).

Comprehenvsive Genome Analysis

The Comprehensive Genome Analysis Service provides a streamlined analysis "meta-service" that accepts raw reads and performs a comprehensive analysis including assembly, annotation, identification of nearest neighbors, a basic comparative analysis that includes a subsystem summary, phylogenetic tree, and the features that distinguish the genome from its nearest neighbors.


The BLAST service uses BLAST (Basic Local Aligment Search Tool) to search against public or private genomes or other databases using DNA or protein sequence(s).

SARS-CoV-2 Genome Assembly and Annotation

The SARS-CoV-2 Genome Assembly and Annotation Service provides a streamlined "meta-service" that accepts raw reads and performs genome assembly, annotation, and variation analysis.

Similar Genome Finder

The Similar Genome Finder Service will find similar public genomes in PATRIC or compute genome distance estimation using Mash/MinHash. It returns a set of genomes matching the specified similarity criteria.


The meta-CATS tool looks for positions that significantly differ between user-defined groups of sequences. However, biological biases due to covariation, codon biases, and differences in genotype, geography, time of isolation, or others may affect the robustness of the underlying statistical assumptions.

Phylogenetic Tree (B)

The Phylogenetic Tree Building Service enables construction of custom phylogenetic trees for user-selected genomes.

Genome Alignment (B)

The Whole Genome Alignment Service aligns genomes using progressiveMauve.

Primer Design

The Primer Design Service utilizes Primer3 to design primers from a given input sequence under a variety of temperature, size, and concentration constraints.

Variation Analysis (B)

The Variation Analysis Service can be used to identify and annotate sequence variations.

Tn-Seq Analysis (B)

The Tn-Seq Analysis Service facilitates determination of essential and conditionally essential regions in bacterial genomes from data generated from transposon insertion sequencing (Tn-Seq) experiments.

Subspecies Classification (V)

The sub-species classification tool assigns the genotype/subtype of a virus, based on the genotype/subtype assignments maintained by the International Committee on Taxonomy of Viruses (ICTV). This tool infers the genotype/subtype for a query sequence from its position within a reference tree. The service uses the pplacer tool with a reference tree and reference alignment and includes the query sequence as input. Interpretation of the pplacer result is handled by Cladinator. Link to pplacer and Cladinator.

MSA and SNP Alignment

The multiple sequence alignment service with variation and SNP analysis can be used with feature groups, fasta files, aligned fasta files, and user input fasta records. If a single alignment file is given, then only the variation analysis is run.

Proteome Comparison

The Proteome Comparison Service performs protein sequence-based genome comparison using bidirectional BLASTP. This service allows users to select genomes and compare them to reference genome.

Gene Tree

The Gene Tree Service is being tested.

Metagenomic Read Mapping

The Metagenomic Read Mapping Service uses KMA to align reads against antibiotic resistance genes from CARD and virulence factors from VFDB.

Taxonomic Classification

The Taxonomic Classification Service computes taxonomic classification for read data.

Metagenomic Binning

The Metagenomic Binning Service accepts either reads or contigs, and attempts to "bin" the data into a set of genomes. This service can be used to reconstruct bacterial and archael genomes from environmental samples.

Expression Import

The Differential Expression Import Service facilitates upload of user-provided, pre-processed differential expression datasets generated by microarray, RNA-Seq, or proteomic technologies to the user's private workspace.

RNA-Seq Analysis

The RNA-Seq Analysis Service provides services for aligning, assembling, and testing differential expression on RNA-Seq data.

ID Mapper

The ID Mapper tool maps PATRIC identifiers to those from other prominent external databases such as GenBank, RefSeq, EMBL, UniProt, KEGG, etc. Alternatively, it can map a list of external database identifiers to the corresponding PATRIC features.

Fastq Utilities

The Fastq Utilites Service provides capability for aligning, measuring base call quality, and trimmiing fastq read files.