MapOptics v2.0

MapOptics v2.0

Following user community feedback that MapOptics is slow to load and can crash using large datasets, MapOptics has been redesigned to address these issues.

MapOptics v2.0 is being released to highlight the incredible improvements to the speed of loading and interacting with the optical mapping datasets. Currently the GUI and functions of MapOptics will look very similar to MapOptics v.0.1.10 but the performance has been enhanced.

Improvements

Time spent loading Xmaps and Cmaps has been significantly reduced and memory usage has been reduced by over 50% compared to MapOptics v.1.10.

These performance gains allow very large datasets with reference genome map 250 Mbp in length and with 1000’s of aligned query contigs to be loaded in seconds, with ease.

MapOptics v2.0 memory usage has been optimised by dynamically storing only data of interest with respect to the reference contig chosen.

This is coupled with a streamlined sorting query contig algorithm which lays out the query contigs in a manner that the user can see all queries even in heavy overlapping alignment regions, meaning easy navigation between Summary, Reference and Query View with no lag.

Deleted contigs are now stored in such a way to allow fast loading of references that have been modified by the user.

Query View has been improved so that the selected range of interest or the selected Query from Reference View will be drawn and interactable almost instantly.

New Features

SV view tab:
Addition of the SV View tab to allow the visualisation of structural variants between maps (insertions and deletions). For each selected reference the user will be provided with an SV table providing information on all the structural variants present between that reference and its associated queries. Upon selection of the structural variant of interest, the user will be presented with a high-resolution view of the structural variant.

Reference View:
Most recently moved contig is highlighted in Reference View. Not only is the currently selected contig highlighted with a GOLD border in the Reference View, the most recently moved contig is highlighted with a BLUE border to give the user feedback on the contigs they are interacting with.

Export Tables:
New menu option to save the entries in the Query Contigs table (Reference View) and Query labels table (Query View) for user selected References and Queries.

MapOptics v1.0.0 Beta

MapOptics v1.0.0 Beta

Following user community feedback that MapOptics is slow to load and can crash using large datasets, MapOptics has been redesigned to address these issues.

MapOptics Beta is being released to highlight the incredible improvements to the speed of loading and interacting with the optical mapping datasets. Currently the GUI and functions of MapOptics will look very similar to MapOptics v.0.1.10 but the performance has been enhanced.

Please note this Beta release does not contain all the original functionality of MapOptics v.0.1.10, this is in process of being fully restored.

To use the Beta version, switch to MapOptics_Beta branch and download the mapOptics_2020_GP.jar

Improvements

Time spent loading Xmaps and Cmaps has been significantly reduced and memory usage has been reduced by over 50% compared to MapOptics v.1.10.

These performance gains allow very large datasets with reference genome map 250 Mbp in length and with 1000’s of aligned query contigs to be loaded in seconds, with ease.

MapOptics Beta memory usage has been optimised by dynamically storing only data of interest with respect to the reference contig chosen.

This is coupled with a streamlined sorting query contig algorithm which lays out the query contigs in a manner that the user can see all queries even in heavy overlapping alignment regions, meaning easy navigation between Summary, Reference and Query View with no lag.

Deleted contigs are now stored in such a way to allow fast loading of references that have been modified by the user.

Query View has been improved so that the selected range of interest or the selected Query from Reference View will be drawn and interactable almost instantly.

New Features

The Beta release has been about improvements to the code underlying MapOptics, but there are a couple of new features.

In Reference View:

Most recently moved contig is highlighted in Reference View:

• Not only is the currently selected contig highlighted with a GOLD border in the Reference View, the most recently moved contig is highlighted with a BLUE border to give the user feedback on the contigs they are interacting with.

In Query View:

• Query View has a reorientation button- allowing the user to change the orientation (+/-) of the query contig to the reference contig.

Export Tables:

New menu option to:

• Save the entries in the Query Contigs table (Reference View) and Query labels table (Query View) for user selected References and Queries.

MapOptics

Initial release of MapOptics Version 0.1.10