Ridom SeqSphere+ version 10.0
Introduction
- Overview
- Core Genome MLST
- Citations and Licenses
- Product Features
- Licensing Model
- Long-read Data Plasmid Transmission Analysis Module
- ONT Data Assembly Module (beta)
- Consortium Server
- 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
- SARS-CoV-2 Analysis Quick Start
- Main Window
- Metadata
- 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
Projects
- 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
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 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
- Encryption