Ridom SeqSphere+

Software Features


Client/server architecture

The client/server architecture allows distributed workgroups to cooperate via intra- or internet. Multiple users can access the data from various computers. Access rights and privileges can be configured to restrict access for specific users.

DNA re-sequencing editor

Assemble raw reads (FASTQ) with integrated Velvet, SPAdes, and BWA algorithms. Read and analyze assembly files (ACE, BAM, FASTA). Autocorrect homo-polymer related InDel errors. Edit and analyze NGS or Sanger DNA sequence data.


Editor for NGS data

Pipeline for automated sequence analysis

Define and start a pipeline to trim by quality, down-sample, assemble, analyze, and type hundreds of NGS data at once automatically; e.g. by fetching raw reads from the benchtop sequencer as soon as data are generated. Define quality criteria (e.g., % of good cgMLST targets) for sample success. Correct handling of repeated samples is built-in to the pipeline.

Characterize bacteria

Characterize bacteria Type bacteria automatically with user defined QC parameters (e.g., coverage or frame shift). Genome- wide allele and SNP calling from WGS data either on core genome and/or accessory genome level is implemented. Use public schemes for genotyping or define them by using the incorporated cgMLST Target Definer. User-defined virulome and resistome analysis is also supported.


Minimum Spanning Tree

Database

Store, search, retrieve, export, and create reports from experiment, epidemiologic, and DNA sequence data stored in an integrated database. Data fields are compliant with the meta-data requirements of the EBI European Nucleotide Archive (ENA). Compare new sequence entries against stored data. Get automatically cluster alerts of possible outbreaks. Manage and backup all data (sequence and epi-data). Download from NCBI complete/draft genomes or SRA reads. Submit with just one click raw read- and epi-data to EBI ENA.


Editor for database fields

Analytical tools

Visualize place, time, ‘person’, and type dimensions in a comparison table with built-in GIS, epi-curve, and phylogenetic tree (among others the minimum spanning tree algorithm is supported) functionality (Fig. 3). All dimension views are inter-linked and exportable in publication quality format (SVG and EMF). Store tree coloring, topology, and selection of samples in a comparison table snapshot. Search for group-specific SNPs, e.g., for designing an outbreak-strain specific PCR screening assay.


Place, time, 'person' and type dimension visualized

Community

Download certified typing schemes online. Rapidly and easily share typing schemes with others. Contribute optional to the world-wide expanding publically available cgMLST.org server of allele nomenclature. Request a non-public epi- demiologic data server for a closed group of users.

Security

Encryption (SSL) of all data in transmission. Configurable anonymization of meta-data like place and time before making data public (cgMLST.org or ENA submission). Various configurable user roles, user groups and access controls. Audit trail functionality (who did, what, and when).


System Requirements

Microsoft Windows 64-bit or Linux 64-bit, quad-core processor, 16-32 GB RAM, >1 TB harddisk (depending on the amount of data that should be stored). See the SeqSphere+ user guide for more detailed system requirements.

Licensing

The license is limited to a time period and a number of named user accounts on the server. Each named user account allows to login once at the same time. If somebody else logs in with the same account, a read-only mode is activated for this session. The Pipeline Mode also runs with a named user accounts but can run concurrently. So the same user can be logged in in the normal mode, and can run several pipelines at the same time. Client software can be installed on an unlimited number of computers. The license period starts with the activation of the license. The license will expire after the defined period and the software runs with read-only access unless a new license is ordered. Read-only access still allows to view and export existing data. License includes updates and support within the time period. Free support includes email as well as online remote (TeamViewer) help. Ridom strives to answer basic support questions the same or the next working day in function of the time zone.

FOR RESEARCH USE ONLY.


 
  Copyright © Ridom GmbH, Germany   Last modified: 12-Apr-2017  Imprint