DASHit: Guide design for DASH experiments
DASHit is a collection of software for the automated design and evaluation of Cas9 guide RNAs for DASH experiments (1).
- Gu, W. et al. Depletion of Abundant Sequences by Hybridization (DASH): using Cas9 to remove unwanted high-abundance species in sequencing libraries and molecular counting applications. Genome Biology 17, 41 (2016).
Made in SF with
Please visit http://dashit.czbiohub.org for documentation and examples.
Running via Docker
The fastest way to get started with
DASHit is to run our Docker image. Assuming the sequence files you want to process are in
/home/user/data, simply run the
docker run -it -v /home/user/data:/data czbiohub/dashit bash
Once you're in the container, navigate to the directory containing your sequence files and get started using
cd /data crispr_sites ...
See http://dashit.czbiohub.org for complete documentation and examples of guide design.
If you're already running
DASHit via Docker you're done! Visit http://dashit.czbiohub.org for examples showing how to run
If you don't want to run
DASHit with Docker, here are instructions for installing from source.
DASHit runs on Linux and macOS.
- A C++ compiler that supports C++11, e.g., a recent version of
goversion 1.9 or later
- (Optional, but recommended) seqtk is a useful tool for manipulating FASTQ/A files. Once you compile
seqtk, place it in your
install seqtk /usr/local/bin)
On macOS, the quickest way to install
python3 is via homebrew. Once homebrew is installed, you can run
brew install python brew install go # The xcode command line utilities will install clang xcode-select --install
On Linux, download and install go here, and then install
python3 via your distributions package manager. On Ubuntu, this is
sudo apt-get update sudo apt-get install build-essential sudo apt-get install python3-pip
Then, to install DASHit:
git clone https://github.com/czbiohub/dashit cd dashit python3 -m venv ~/.virtualenvs/dashit source ~/.virtualenvs/dashit/bin/activate # Run the following two commands separately make sudo make install
By default this will install compiled binaries into
/usr/local/bin. To specify a different location for these compiled
PREFIX=$HOME make install
Note: At least the
vendor/special_ops_crispr_tools/offtarget/offtargetbinary must be in your
PATHin order for
To test that everything installed correctly, open up a new shell, activate the virtualenv and take DASHit for a spin:
source ~/.virtualenvs/dashit/bin/activate dashit_filter --help crispr_sites -h optimize_guides echo "AAAAAAAAAAAAAAAAAAAA" > /tmp/mysequence.txt && HOST=file:///tmp/mysequence.txt offtarget
CTRL+C to exit
Copyright 2019 Chan-Zuckerberg Biohub
Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at
Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.
Previous versions of DASHit were licensed under the hybrid Biohub License, which was free for non-profit use, but required a separate agreement for commercial use.