CRISPR Software Matchmaker
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-- Readme --
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Welcome to the CRISPR Software Matchmaker.
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This resource is the work of a small project aimed at making the choice between various CRISPR software tools a little easier; secondly, to help inform developers on where to focus their efforts next. Because CRISPR reaches into so many diverse communities the best person to review the various tools is you. That is why each tool has been objectively evaluated by whether or not it has 1 of 65 features. Each feature is an aspect of CRISPR sgRNA design that may or may not be important to you; it is up to you to decide. There are 5 tabs: the Main tab is where the magic happens, but it is advised to go to the Summary and Glossary tabs first in order to get a good feeling for how things work. After reading about the tabs below you should also see if any of the notes apply to you. This spreadsheet should be viewed as a community project, a work in progress that will grow and get better through your input. It is a Google Sheet for practical reasons: to allow everyone to view, copy, and edit it. Keep in mind that editing is strictly limited to the copies you make in your own Google Drive. Suggestions to improve this resource should be emailed along with access to view your own copy to demonstrate your change.
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last updated on: 26/11/2015 (d/m/y)
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-- Tabs ---- Notes --
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SummaryHow features were determined
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The Summary tab provides a table with a normalised feature count for each tool. The features are separated into 8 categories that describe basic to advanced functions as well as how the user is expected to use/interface with the software. This tab is meant to provide an overview and determine which (if any) tool is most feature rich in which category. This is a good place to start if you are just getting familiar with how this spreadsheet works. Within the Summary tab, if you hover your mouse over a category then a definition for it will appear as a popup message. Likewise, if you hover your mouse over a tool then a link to the tool's website will appear. While this Summary tab is useful, please use the Main tab in order to select the tool that best suits your needs.Features were determined by reviewing the tools in chronological order by date of publication, as new functions were introduced over time a new feature was added and defined. Previously reviewed tools were then retroactively updated, if required. This method means that the features listed reflect only the current software space and not all features pertinent to CRISPR sgRNA design. If a feature is required but not listed here it is highly likely that there is currently no software that supports it (yet). In the event that a feature was inadvertently overlooked, and you are an author of the tool, please send an email and it will gladly be corrected.
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MainAvailable organisms
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The Main tab is a large table describing whether or not a tool (row) has a feature (column). The size of the table may be confusing at first, but keep in mind that at its heart it is a simple binary mapping: if tool T has feature F then you will see a "1" in the cell and the cell will be colored blue; if not, then the cell will contain a "0" and be colored grey. Sometimes a tool doesn't match the feature definition perfectly and rather than create a new feature it is given a score of "0.5" and colored light blue. As in the Summary tab, hovering your mouse over any feature will provide its definition (the same definition as can be found in the Glossary tab). The point of this table is to find the software that has most/all of the features you need. Since the table is so large, to help with this task a row labeled "Weight" and a column labeled "Score" has been added. If you change the weights of features from 0 to some value you feel defines the relative importance of that feature to your project then the scores for each tool will be updated to reflect your opinion (read, "How to use the table interactively", for more information). The 8th feature category is a catalogue of organisms supported by CRISPR tools labeled as genome assembly names coupled with versions. Many of the feature names are equivalent as they reflect the names chosen by the authors of the software tools themselves. The organisms have currently been separated into vertebrates, insects, plants/algae/moss, fungi, and other. There is currently no other ordering (alphabetic or otherwise). This may change over time.
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GlossaryDevelopers / Authors
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A glossary of all the terms used in this document. New terms and/or better definitions may be suggested by email along with access to view your own copy to demonstrate your change.As this resource is new, accuracy is of utmost importance. Developers who wish to amend/query feature associations or otherwise add new features are invited to email their suggestions at any time.
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ExampleHow to use the table interactively (see tab: Example)
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The Example tab is a modified copy of the Main tab. The feature weights have been changed to reflect the opinion of someone using CRISPR to edit the genome of Plasmodium falciparum 3D7 (causes malaria, is AT rich at >80%, doesn't have NHEJ). This tab will demonstrate how assigning value to different features reflects in the score of each tool. A detailed reasoning behind the choice of weights is also provided.To use this resource interactively, as demonstrated by the Example tab, you will need to copy this file to your own Google Drive. You can do this from the 'File' menu. Only then will you have permission to edit the file. If you make a mistake, don't worry, simply copy the file again to reset.
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This Google sheet was built to support the Addgene blog post entitled, "CRISPR software and the Piñata Effect".
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link to blog post
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To get in contact with the author, please email Cameron MacPherson at:
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protospacer.cas9@gmail.com
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last updated on: 26/11/2015 (d/m/y)