Ridom SeqSphere+ version 7.2

Introduction

Overview
Core Genome MLST
Citations and Licenses
Product Features
Licensing Model
Contact

Installation

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
Tutorials
Main Window
Metadata
Core Genome MLST Schemes
Core Genome MLST Complex Type
Submission to cgMLST.org
Quality Management of WGS Data
De Novo Assembler Evaluation

Projects

Managing Projects
Database Schemes for Storing Epidemiological Data

Task Templates

Core Genome MLST/Accessory Task Templates
MLST Task Templates
Resistance/Virulence Task Templates
Geno-Serotyping Task Templates
Spa-Typing Task Template
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

Tools

Comparison Table
Sample QC Statistic
Search Similar Samples in Database
cgMLST Target Definer
Database Overview
Reprocess Samples
Manage Submission to cgMLST.org
Position Navigator
Download from NCBI Genomes
Download FASTQ from NCBI SRA
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)

Access Control and Security

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

Appendix

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