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File Upload

Canu Assembler

Species Identification

Virulence Estimation

AMR Detection

Overview

Step 1: Choose Analysis and Upload File

Upload a third-generation sequencing (such as the PacBio RS II or Oxford Nanopore MinION) in FASTA format (2 GB limit).
We will email you a link to your page with your quality assessment reports.
We will also notify you when your report is finished, and contact you if any problems arise.

Step 2: A single molecule sequence assembler for genomes

Canu v1.4

Named by prefix of file
Maximum number of compute threads to use by any component of the assembler
An estimate of the size of the genome

Step 3: Bacterial species identification

NCBI nt database

Upload the genome assembly components (contigs, scaffolds, chromosomes) in FASTA format (10 MB limit).
-e e-value cutoff for prediction

Step 4: Bacterial virulence estimation

VFDB: Virulence Factors Database

-e e-value cutoff for prediction
% sequence completeness between the query and subject virulence-related sequences

Step 5: Antibiotic resistance detection

CARD: The Comprehensive Antibiotic Resistance Database

-e e-value cutoff for prediction
% sequence completeness between the query and subject antibiotic-resistant sequences

Step 6: Overview

To make any necessary changes before submitting click on the tabs/steps above.
The title of the submission
-e e-value cutoff for NCBI
-e e-value cutoff for VFDB
-e e-value cutoff for CARD
Named by prefix of file
Maximum number of compute threads to use by any component of the assembler
An estimate of the size of the genome