Ridom SeqSphere+ version 10.0


Core Genome MLST
Citations and Licenses
Product Features
Licensing Model
Long-read Data Plasmid Transmission Analysis Module
ONT Data Assembly Module (beta)
Consortium Server


Installing and Initializing
System Requirements
Required Network Connections
WGS Data Types & Sizes and Runtimes
Server Administration
Database Backups
Updating the Software

Getting Started

Getting Started with SeqSphere+
SeqSphere+ General Procedure
SARS-CoV-2 Analysis Quick Start
Main Window
Core Genome MLST Schemes
Core Genome MLST Complex Type
Submission to cgMLST.org
Long-Read Data Processing
Quality Management of WGS Data
De Novo Assembler Evaluation


Managing Projects
Database Schemes for Storing Epidemiological Data
Local Single Linkage Clustering IDs
Early Warning Alerts

Task Templates

Core Genome MLST/Accessory Task Templates
MLST Task Templates
Resistance/Virulence Task Templates
Geno-Serotyping Task Templates
Chromosome and Plasmids Overview Task Template
CGE MobileElementFinder Task Template
Mash Plasmid Typing Task Templates
Spa-Typing Task Template
SARS-CoV-2 Task Templates
Managing of Task Templates
Target Parameters
Genotyping Libraries
Genotyping Result Fields
Manage Allele Libraries

Assembling Pipelines

Pipeline Mode
Pipeline Script
Pipeline Report
Sequencing Run Details

Samples and Task Entries

Process Assembled Genome Data
Process Sanger Sequencing Data
Import Epi Metadata
Managing Samples
Sample Overview
Task Entry Overview
Target Overview
Contig Sequence Editor
Project Overview Table
Export Assembly Contigs (FASTA, ACE/BAM)
Export Metadata
Creating Sample Reports
Download Complete and Draft Genomes from NCBI

Comparison Tables

Comparison Table
Comparison Table Snapshot
Comparison Table Retrieval
Neighbor Joining Tree
Minimum Spanning Tree
Geographical Map
Epi Curve
Find SNVs
Find Group Specific SNVs


Comparison Table
Sample QC Overview
Search Similar Samples in Database
cgMLST Target Definer
Database Overview
Reprocess Samples
Position Navigator
Manage Submission to cgMLST.org
Download from NCBI Genomes
Download FASTQ from NCBI SRA
Download Samples from cgMLST.org/Consortium
Submit Samples to EBI ENA
Submit Samples ECDC TESSy

Genome Utilities

Identification (Mash Distance)
Contamination Check (Mash Screen)
Genome Similarity (FastANI)
FASTQ Quality Control (FastQC)
Illumina Adapter Trimming (Trimmomatic)
Read Mapper (BWA)
Paired-End Library Insert Sizes (Picard)
Read Assembler (Velvet)
Fix Start and Orientation for Plasmids or Chromosomes
Comparison and Visualization of GenBank-Files (pyGenomeViz)

Access Control and Security

Managing Users
Access Control
Change Password and User Settings
Sample Audit Trail
Access Logging


Administrator Guide
Complete Version History
Windows Subsystem For Linux
Command Line Parameters
SPEC Files
Similarity Search Result Columns
Regular Expressions
Codon Translation Tables
Glossary of Terms