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).

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 ♥️ and 🔬 by the Biohub Data Science Team.

Documentation

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 DASHit image

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 DASHit!

cd /data
crispr_sites ...

See http://dashit.czbiohub.org for complete documentation and examples of guide design.

Installation

If you're already running DASHit via Docker you're done! Visit http://dashit.czbiohub.org for examples showing how to run DASHit.

If you don't want to run DASHit with Docker, here are instructions for installing from source. DASHit runs on Linux and macOS.

Dependencies

Installing DASHit requires

1. A C++ compiler that supports C++11, e.g., a recent version of g++ or clang
2. go version 1.9 or later
3. python3
4. (Optional, but recommended) seqtk is a useful tool for manipulating FASTQ/A files. Once you compile seqtk, place it in your PATH (e.g., install seqtk /usr/local/bin)

On macOS, the quickest way to install go and 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 g++ and 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

DASHit

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 binaries, set PREFIX, e.g.,

PREFIX=$HOME make install

Note: At least the vendor/special_ops_crispr_tools/offtarget/offtarget binary must be in your PATH in order for dashit_filter to work.

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

Press CTRL+C to exit offtarget.

License

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

http://www.apache.org/licenses/LICENSE-2.0

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

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.