Ridom SeqSphere+ version 4.0
Introduction
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+
- Tutorials
- Main Window
- Metadata
- Core Genome MLST Schemes
- Core Genome MLST Cluster Type
- Submission to cgMLST.org
- Quality Management of WGS Data
Projects
Task Templates
- Managing Task Templates
- Target Parameters
- Genotyping Libraries
- Genotyping Result Fields
- Manage Allele Libraries
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 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
Assembling Pipelines
Tools
- Comparison Table
- Sample QC Statistic
- Search Similar Samples
- cgMLST Target Definer
- Submit Samples to EBI ENA
- Download FASTQ from NCBI SRA
- Database Overview
- Reprocess Samples
- Position Navigator
- BWA Mapper
- Velvet Assembler
- SPAdes Assembler
Access Control and Security
Appendix
- Preferences
- Default Database Scheme for Storing Epidemiological Data
- Procedure Details
- Procedure Statistics
- SPEC Files
- Glossary of Terms
- Similarity Search Result Columns
- Regular Expressions
- Command Line Parameters
- Administrator Guide
- FAQ