Table of Contents : Miscellaneous :
Hints & tips | BENCHlab Integration | Menus

BENCHlab integration

Alamut® Visual offers a strong and secured integration with the BENCHlab NGS platform marketed by Cartagenia:

The regular Alamut® Visual software can be connected to BENCHlab
An embedded version of Alamut® Visual - marketed by Cartagenia - is dedicated to work along and only with BENCHlab

From BENCHlab to Alamut® Visual

BENCHlab enables the user to click on a variant from a BENCHlab analysis and to get the appropriate gene transcript loaded in Alamut® Visual, displaying automatically a variant window (Alamut® Visual must be launched prior to this process).

When a transcript version is not available in Alamut® Visual, the closest transcript is displayed.

BENCHlab managed variant lists

When connected to BENCHlab, Alamut® Visual holds an extra menu ('Folders' > 'BENCHlab Variants') which provides the managed variant lists available in BENCHlab. This feature enables the user to display within Alamut® Visual the variants collected from BENCHlab. This menu works similarly as the one for variants (see Where and how variants are stored).
In a future version, it will also be possible to save variants in BENCHlab's managed variant lists.

Limitations of the embedded Alamut® Visual version

When embedded in BENCHlab, Alamut® Visual has some functional limitations (which do not exist in the regular version):

To operate, Alamut® Visual requires BENCHlab to run concurrently and continuously.
Therefore, when BENCHlab is disconnected, Alamut® Visual is automatically inactivated. Afterwards BENCHlab needs to be reconnected before the user can use Alamut® Visual again.
User variants cannot be saved locally. Therefore, the menu 'Folders' > 'Variants' does not exist in this version.
In a future version, it will be possible to save variants in BENCHlab's managed variant lists.
Variants cannot be imported from cDNA, gDNA or VCF files, or exported from Alamut® Visual as well. Therefore, the menus 'Variants' > 'Export internal variants...' and 'Variants' > 'Delete all internal variants...' do not exist in this version.

All standard Alamut® Visual annotations and analysis (e.g., nomenclature, consequences, missense and splicing predictions) are available in the embedded version.