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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).
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).
Allows to set some country specific defaults.
User Interface Size
Allows to increase the size of fonts and button icons.

Comparison Table

Distance Calculation
Allows to hide the warning dialog for columns with empty values
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
You can specify the default Submission Anonymization Filter to define what level of place/time and sample ID should submitted to public databases. The defined filter for will be used as default when creating a new pipeline script.

Input Files

BAM are produced by SKESA/SPades pipelines with de novo remapping enabled, and by BWA pipelines.
SeqSphere can also import SAM/BAM files from other sources.
The following settings can be specified here for reading SAM/BAM files:
  • Discard reads with a mapping quality lower than a defined threshold (default 10)
  • Ignore illegal reads (e.g., bad cigar string). If this option is disabled, the processing of the BAM file aborts with an error if illegal reads are found reads that are marked to have more than one best hit (X0 tag > 1) or as secondary alignment (bitwise FLAG)
  • Discard reads that are marked as PCR or optical duplicate (bitwise FLAG)