General
- Memory Usage
- Configure the maximum of memory (RAM) that can be used by SeqSphere+. On 32bit operating systems this maximum is limited to around 1.3 GB. On 64bit systems it is only limited by your physical available memory. A minimum of 4 GB is recommended for those systems. The default value is 1/4th of the physical memory. The assemblers that are called in the pipeline are running in an external process and are therefore not limited by this maximum. However, there must be enough physical memory left available for those external processes. Increase the maximum of memory (RAM) that can be used by SeqSphere+ above the default value only if you want to process or load a large number of Samples or if you want to create very large Comparison Tables.
- Temporary Folder
- Allows to change the temporary folder that is used by SeqSphere for all temporarily created files (e.g., for large temporary assembling data).
- Login
- Allows to disable showing the last used login name as default in the login dialog (e.g., if the SeqSphere client is used by multiple users).
- Localization
- Allows to set some country specific defaults.
- PDF Viewer (Linux version only)
- If your standard PDF Viewer is not found automatically it can be specified here.
Comparison Table
- Distance Calculation
- Allows to hide the warning dialog for columns with empty values
- Highlight
- Allows to disable the highlighting of empty values
DNA Sequence Views
- Contig Alignment
- You can specify if the visible layout of the aligned read rows when scrolling through the contig alignment.
- Sequence Editor
- You can specify the color schemes visible layouts for the sequence and chromatogram editors
- Read Import
- You can specify if the name of a read should be take from the file name, or from an internal comment
Online Connection
- Proxy Server
- The Proxy settings must be specified here if your need to go through a HTTP Proxy to access the Internet.
- Online Updates
- You can specify if SeqSphere+ should search for updates on every startup.
- Sample Submission to cgMLST.org/ENA
- You can specify the Submission Anonymization Filter to define what level of place/time and sample ID should submitted to public databases.
Input Files
- SAM/BAM
- Reads with a mapping quality below the given threshold (default 10) are discared when Samples are created from SAM/BAM files using Process Assembled Genome Data or the Pipeline Mode.