From b5a7f91d1313d97b6dc983c082a5c72e87de4d5e Mon Sep 17 00:00:00 2001 From: Carl Schmitz Date: Mon, 19 Feb 2024 14:34:09 +1000 Subject: [PATCH] Updated README --- README.md | 25 ++++++++++++------------- 1 file changed, 12 insertions(+), 13 deletions(-) diff --git a/README.md b/README.md index d403c7c..04e4f6d 100644 --- a/README.md +++ b/README.md @@ -5,19 +5,18 @@ Rapid Whole-Genome Identification of High Quality CRISPR Guide RNAs with the Cra ## Preamble -> The design of CRISPR-Cas9 guide RNAs is not trivial. In particular, evaluating the risk of off-target -modifications is computationally expensive: a brute-force approach would require comparing each candidate -guide with every possible CRISPR target site in the genome. In a mammalian genome, this means hundreds of -millions of comparisons for each guide. We have previously introduced Crackling, a gRNA design tool that -relies on Inverted Signature Slice Lists (ISSL) to accelerate off-target scoring by only considering sites -with partial matches (a slice) with the candidate guide. This produced an order of magnitude speed up whilst -still maintaining scoring accuracy. Here, we present a complete reimplementation of Crackling in C++ and -discuss further improvements. Using longer slices means fewer comparisons, and we show it is possible to -construct a collection of slices that still preserve an exact off-target score. We have benchmarked two ISSL -configurations with the new version of Crackling and report a 15-22 times speed up over the default ISSL -configuration. This increased performance comes at the cost of increased memory usage, but this can be offset -by using memory mapped files, and we show that this has no significant impact on performance. -CracklingPlusPlus is available at https://github.com/bmds-lab/CracklingPlusPlus under the Berkeley Software +> The design of CRISPR-Cas9 guide RNAs is not trivial. In particular, it is crucial to evaluate +the risk of unintended, off-target modifications, but this is computationally expensive. To +avoid a brute-force approach where each guide RNA is compared against every possible CRISPR +target site in the genome, we previously introduced Crackling, a guide RNA design tool that +relies on exact matches over 4bp subsequences to approximate a neighbourhood and accelerate +off-target scoring by greatly reducing the search space. While this was faster than other +existing tools, it still generates large neighbourhoods. Here, we aim to further reduce the +search space by requiring more, now non-contiguous, exact matches. The new implementation, +called Crackling++, is benchmarked against our initial approach and other off-target evaluation +tools. We show that it provides the fastest way to assess candidate guide RNAs. By using memorymapped +files, it also scales to the largest genomes. +Crackling++ is available at https://github.com/bmds-lab/CracklingPlusPlus under the Berkeley Software Distribution (BSD) 3-Clause license. ## Dependencies