SeqSphere+
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Application data |
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| Created by | Jörg Rothgänger, Dag Harmsen |
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| Biological application domain(s) | Comparative genomics, Microbial Surveillance |
| Principal bioinformatics method(s) | Sequence assembly, Read mapping, Variant calling |
| Technology | Sanger, Illumina, 454, Ion Torrent, PacBio |
| Created at | Ridom GmbH (Münster, Germany), http://www.ridom.de |
| Maintained? | Yes |
| Input format(s) | FASTA, FASTA+QUAL, BAM, ACE, GenBank, SCF, ABI |
| Output format(s) | FASTA, BAM, ACE, SCF |
| Software features | Advanced and user-friendly analyses of genomic microbial NGS and Sanger data |
| Programming language(s) | Java |
| Software libraries | Stand-alone version |
| Licence | Commercial |
| Operating system(s) | Windows, Linux 64 |
| Contact: | info@ridom.de |
Summary: Ridom SeqSphere+ Software is designed for distributed work-groups (client/server model) and allows automatic processing, assembling and analyzing of NGS (e.g., Illumina, Ion Torrent or PacBio) and Sanger capillary-electrophoresis sequence data. SeqSphere+ is the solution for easy and automated microbial analysis; enabling your lab to employ whole genome microbial typing (cgMLST or MLST+), traditional MLST or eMLST/rMLST sequencing projects.
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Description
With fast and affordable microbial whole genome shotgun (WGS) next generation sequencing and automatized software analysis, microbiologists can use genome-wide hundreds/thousands of genes (core genome MLST or MLST+) for typing, resulting in higher discrimination and more accurate strain typing. The heightened discrimination power of MLST+, coupled with rapid and simple workflow NGS, makes SeqSphere+ the complete solution ideal for everyday microbial monitoring to outbreak investigation, e.g. MRSA hospital outbreak (JCM 52: 2365, 2014). Various tools available for genomic surveillance have been reviewed recently (Pathogens 3: 437, 2014). That is, one disruptive technology that fits any bacteria and any study type is finally within reach for any microbiologist/laboratory.
DNA re-sequencing editor: Assemble (FASTQ reads), edit and analyze your NGS or Sanger DNA sequence data. Read assembly files (ACE & BAM). De novo assemble or reference map NGS read data with integrated Velvet or BWA, respectively. Autocorrect homo-polymer related InDel errors.
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 the raw reads from the benchtop sequencer as soon as data are generated. Define quality criteria (e.g., % of good MLST+ targets) for sample success. If initially failed the pipeline is able to handle repeated samples accordingly.
Type bacteria: Type bacteria (e.g., spa, MLST, MLST+) automatically with user defined parameters (e.g., coverage, intragenic stop codons, frame shift detection). Use public or quickly self define schemas for genotype, virulome and/or resistome analysis by using the incorporated MLST+ Target Definer functionality.
Database: Store, search, retrieve, export and create reports from your epidemiologic and DNA sequence data stored in an integrated database. Data entry plausibility check is possible. Data fields are compliant with the meta-data requirements of the EBI ENA archive. Compare new sequence entries against stored data. Get automatically cluster alerts of possible outbreaks. Manage and backup all of your sequencing data (raw reads, assemblies, etc.). Submit with just one click raw read data to EBI ENA.
Analytical tools: Select data entries from a comparison table for epidemiologic, evolutionary or functional analysis. Cluster and visualize allelic profiles by using minimum spanning or UPGMA/Neighbor Joining trees. Export trees in publish ready scalable vector graphics (SVG) format. Export concatenated core/accessory genome gene sequences for further analysis.
Security/Privacy: Encryption (SSL) of all data in transmission. Various configurable user roles, user groups and access controls. Audit trail functionality (who, what and when). Meta-data like place & time can be anonymized for public submission.
Links
References
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