Table 1.
Comparison among different LIMS systems
| LIMS software | MendeLIMS | GNomEx | Galaxy LIMS | QTREDS |
|---|---|---|---|---|
| Clinical study patient samples | ||||
| Patient data (gender/race, MRN, pathology, histology) | Yes | No | No | No |
| Sample processing (dissections, extractions) | Yes | No | No | Yesa |
| Sample location tracking | Yes | No | No | Yes |
| Arrays, libraries, sequencing runs | ||||
| Molecular assays (genomic arrays, ddPCR, ..) | Yes | Yes | No | Yes |
| Sequencing library prep (singleplex and multiplex) | Yes | Yes | Yes | Yesb |
| Flow cell/sequencing run setup | Yes | Yes | Yes | No |
| Post-sequencing analysis | ||||
| Sequencing QC | Yes | nd | Yesc | No |
| Analysis workflow | No | Yes | Yesc | No |
| Security/Audit trail | ||||
| Authorization via user roles | Yes | Yes | Yes | Yes |
| Audit trail | Yes | Yes | nd | nd |
| HTTPS/SSL security | Yes | nd | nd | Yes |
| General | ||||
| Email/notification capability | Yes | Yes | Yesc | Yes |
| Customizable lists for data validation | Yes | Yes | Yes | Yes |
| Instrument integration | No | No | Yesd | No |
| Attach files to samples/libraries/sequencing runs | Yes | nd | No | nd |
| Visualization of results | No | Yese | Yesc | No |
| Other | ||||
| Project based billing | No | Yes | No | No |
| Reagent inventory management | No | No | No | Yes |
| Publicly available User Guide/Demos | Yes | Yes | No | Yes |
a)Detailed information tracked regarding sample prep; b)Singleplex libraries only; c)Functionality provided via integration with Galaxy and genome browsers; d)Integration with HiSeq 2000 only; e)Functionality provided via integration with GenoPub.
nd - Indicates that unable to determine from public documentation whether the functionality is provided.