Tools

Genome Assembly

Allows single or multiple assemblers to be invoked to compare results. The service attempts to select the best assembly.

Genome Annotation

Provides annotation of genomic features using the RAST tool kit (RASTtk) for bacteria and VIGOR4 for viruses. Accepts a FASTA formatted contig file and an annotation recipe based on taxonomy.

Comprehensive Genome Analysis

A streamlined meta-service that accepts raw reads and performs assembly, annotation, identification of nearest neighbors, a subsystem summary, phylogenetic tree, and features that distinguish the genome from its nearest neighbors.

BLAST

Uses BLAST (Basic Local Alignment Search Tool) to search against public or private genomes or other databases using DNA or protein sequences.

Similar Genome Finder

Finds similar public genomes or computes genome distance estimation using Mash/MinHash. Returns a set of genomes matching the specified similarity criteria.

Taxonomic Classification

Computes taxonomic classification for read data using a k-mer-based approach to rapidly assign taxonomy to metagenomic reads.

Metagenomic Binning

Accepts reads or contigs and attempts to bin the data into a set of genomes. Can be used to reconstruct bacterial and archaeal genomes from environmental samples.

Metagenomic Read Mapping

Uses KMA to align reads against antibiotic resistance genes from CARD and virulence factors from VFDB.

Core Genome MLST

Performs core genome multilocus sequence typing (cgMLST) for high-resolution genotyping and clustering of microbial genomes.

Whole Genome SNP Analysis

Identifies whole-genome single nucleotide polymorphisms (SNPs) across a set of genomes for phylogenetic analysis and outbreak investigation.

Bacterial Genome Tree

Enables construction of custom phylogenetic trees for user-selected bacterial genomes using conserved marker genes.

Viral Genome Tree

Enables construction of custom phylogenetic trees for user-selected viral genomes using conserved marker genes.

Gene/Protein Tree

Builds phylogenetic trees from user-selected genes or proteins using multiple sequence alignment and standard tree-building methods.

MSA and SNP Analysis

Performs multiple sequence alignment with variation and SNP analysis on feature groups, FASTA files, aligned FASTA files, or user-provided sequences.

SARS-CoV-2 Genome Analysis

A streamlined meta-service that accepts raw reads and performs genome assembly, annotation, and variation analysis for SARS-CoV-2.

SARS-CoV-2 Wastewater Analysis

Analyzes wastewater sequencing data to detect and quantify SARS-CoV-2 variants for community-level surveillance.

Viral Assembly

Assembles viral genomes from sequencing reads using methods optimized for the characteristics of viral genomes.