Under the Hood

Under the Hood

This series of posts is about a set of major changes that will be happening under the hood of the sRNA Workbench.

These changes have a single and specific aim; to reduce the memory footprint of the workbench.

One of the major problems facing the workbench in its current state (and a large proportion of bioinformatic tools in my opinion) is the amount of RAM required to process and analyse large datasets.

While single dataset size is unlikely to increase (that is one sample that forms part of an experiment) unless the research requires a deeper than normal sequencing depth. The overall size of an entire experiment is increasing and continues to do so. As the cost of producing such data decreases, the volume will increase (a problem that is mentioned time and time again).

As more complex analysis tools are added and the features of existing tools are improved the amount of memory required to run the workbench is increasing. Therefore, a major goal over the coming development period is to drastically reduce this need for resources for all existing tools in the workbench and any new tools that are added.

Interested users can follow the changes in the posts that are made on each release that contains a new version of the tool. Also if you download the new versions of the software and use the new tools you can really help by reporting problems you have found with them.

Links to posts on the new tools can be found below and will be updated as they are ready:

Adapter Removal Low Memory