cgMLST/SNP
WGS-typed bacteria
Micro Solutions / Life Science
Microbial genomics software Ridom SeqSphere+
cgMLST/SNP typing bacteria from WGS data for epidemiological surveillance and outbreak investigation
Product overview
- Ridom SeqSphere+
- Ridom (Bruker)
- Germany
- SeqSphere+
- Ridom SeqSphere+
cgMLST/SNP typing bacteria from WGS data for epidemiological surveillance and outbreak investigation
Formerly known as Ridom SeqSphere+, the current name is Bruker MBioSEQTM Ridom Typer.
Ridom SeqSphere+ is a specialized microbial genomics environment for epidemiological typing, outbreak investigation and surveillance; the current product name is Bruker MBioSEQTM Ridom Typer.
The client-server system automates quality control, assembly of short and long readings, cgMLST/SNP typing, antimicrobial resistance gene identification, genoserotyping and comparison of new isolates to a local base. Linked representations by time, place, object and type, trees and automatic cluster alerts support Epidemiological analysis without writing scripts.
Input: FASTQ from Illumina, PacBio and Oxford Nanopore, as well as Sanger; ACE/BAM/FASTA import. Local SQL database, roles and action audit, SSL and customizable anonymization are supported. Client: Windows 10/11 or 64-bit Linux, 4 cores, 16-32 GB of RAM (for Flye at least 32 GB), 1-2 TB; server: Windows 10/11 or 64-bit Linux, 4 cores, 16 GB of RAM and 1-2 TB disc: The product is for research purposes only.
Key figures
RUO
research-only
4D
time, place, object, type
SQL
local database
Applications
- Epidemiological typing of bacteria
- Outbreak investigation and inpatient supervision
- Identification of antimicrobial resistance genes
- Genoserotyping (Salmonella, E. coli, L. monocytogenes)
- Analysis of clonal and plasmid transmission
Models and configurations
- Ridom SeqSphere+
Product details
WGS-typing workflow
From FASTQ to cgMLST/SNP analysis
4D visualization of results
time, place, object, type
Analysis of data
- Automated conveyor: quality control, assembly of short and long readings (VELVET, SKESA, SPAdes, BWA, Flye, Raven), cgMLST/SNP-typing
- Species identification by GAMBIT and FASTANI; resistance profiling through TB-Profiler and NCBI AMRFinderPlus
- Salmonella (SISTR), E. coli and L. monocytogenes
- Reconstruction and characterization of plasmids (MOB-suite, MobileElementFinder)
Data management and compatibility
- Import FASTQ with Illumina, PacBio, Oxford Nanopore and Sanger; import ACE/BAM/FASTA files
- Download full and draft genomes from NCBI GENOME and readings from NCBI SRA; send data to EBI ENA in one click
- Local SQL database with user roles, action auditing and SSL transfer encryption
- Customizable anonymization of metadata (place, time) before publication in open repositories
Visualization and oversight
- 4D visualization by time, place, object and type in mutually synchronized representations
- Phylogenetic and Minimum Spanning Trees, Exports in Publication Quality (SVG, EMF)
- Automatic notifications of clonal and plasmid transmission when matching the base
- Graphic interface without writing scripts, works on Windows and Linux
Input and typing
| Sequencing platforms | Illumina, PacBio, Oxford Nanopore, Sanger |
|---|---|
| File import | FASTQ, ACE, BAM, FASTA |
| Typed methods | cgMLST, SNP-typing |
| Identification of species | GAMBIT, FASTANI |
| Profiling of resistance | TB-Profiler, NCBI AMRFinderPlus |
| Genoserotyping | Salmonella (SISTR), E. coli, L. monocytogenes |
System Requirements - Customer
| OS | Windows 10/11 (64-bit) or Linux 64-bit |
|---|---|
| Processor | 4 cores |
| RAM | 16–32 GB (for Flye – a minimum of 32 GB) |
| Storage | 1–2 TB |
System Requirements - Server
| OS | Windows 10/11 (64-bit) or Linux 64-bit |
|---|---|
| Processor | 4 cores |
| RAM | 16GB |
| Storage | 1–2 TB (SSD recommended; about 1 TB per 200,000 samples when default settings) |
| Client-server port | 8064 (configuration) |
Data and security
| Database | Local SQL, Roles and Action Audit |
|---|---|
| Encryption | SSL for data transfer |
| Purpose | Research Use Only – Not for Clinical Diagnostics |
Software modules and licenses
1/3/5 year license, 2/5/30 named users
Scaling the number of users and parallel conveyors (up to 75 with 30 users)
Long Read Module (LRM)
Analysis of long readings, including plasmid transmission; included in the license
TB-Profiler AMR
Determination of drug resistance of M. tuberculosis from WGS data
CheckM2
Verification of intraspecific contamination of the sample
GAMBIT Bacterial Species ID
Identification of a species of bacteria not allowed by MALDI-TOF MS
Related equipment types
- MALDI-TOF System for Identification of Microorganisms
- NGS Sequencing (Illumina, Oxford Nanopore)
- Servers and storage for bioinformatics
- LIS for microbiology
Related products
- Bruker MALDI Biotyper sirius — MALDI-TOF System for Identification of Microorganisms
- BGI DNBSEQ-E25 — NGS Sequencing (Illumina, Oxford Nanopore)
- BGI ZTRON — Servers and storage for bioinformatics
Classification
- Sequencing and genotyping
- Bioinformatics and data management
- Equipment for molecular biology and genetics
- Bioinformatics and software
- Epidemiological typing according to WGS
- Ridom SeqSphere+