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


Editor for NGS data

Pipeline for automated sequence analysis

Define and start a pipeline to trim by quality, down-sample, assemble, import, analyze and type hundreds of your NGS raw sequence 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. The batch processing pipeline is also able to handle repeated samples accordingly.

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 supported. Use public schemas for genotyping or self define them by using the incorporated cgMLST Target Definer. Virulome and resistome analysis is also possible.


Minimum Spanning Tree

Database

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


Editor for database fields

Analytical tools

Select data entries from a comparison table for epidemiologic, evolutionary, or functional analysis. Visualize place, time, 'person', and type dimensions with built-in GIS, epi-curve, and phylogenetic tree (among others the minimum spanning tree algorithm is supported) functionality. All dimension views are inter-linked and exportable in publication quality SVG format.


Place, time, 'person' and type dimension visualized

Community

Rapidly and easily share typing schemas with other institutions. Download certified typing schemas online. Option to contribute to a single world-wide expanding publically available server of nomenclature and epidemiologic data. Own server for epidemiologic data for larger (supra) national institutions are on request possible.

Security

Encryption (SSL) of all data in transmission. Optional database and backup encryption. Various configurable user roles, user groups and access controls. Audit trail functionality (who did, what, and when). Meta-data like place and time can be anonymized for public submission.


System Requirements

  • Operating System (64-bit): Microsoft Windows XP/Vista/7/8/10 or Linux (Ubuntu LTS recommended)
  • RAM: 16 GB
  • CPU: Dual-core processor
  • HD: 1 TB (depending on the amount of data that should be stored)
  • Internet connection required

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: 21-Jan-2016  Imprint