Azimuth: Machine Learning-Based Predictive Modelling of CRISPR/Cas9 guide efficiency

References:

• John G. Doench*, Nicolo Fusi*, Meagan Sullender*, Mudra Hegde*, Emma W. Vaimberg*, Katherine F. Donovan, Ian Smith, Zuzana Tothova, Craig Wilen , Robert Orchard, Herbert W. Virgin, Jennifer Listgarten*, David E. Root. Optimized sgRNA design to maximize activity and minimize off-target effects for genetic screens with CRISPR-Cas9. Nature Biotechnology, 2016.

• Azimuth Main Site: https://www.microsoft.com/en-us/research/project/azimuth/
• GitHub Page: https://github.com/MicrosoftResearch/Azimuth

• Module Name: Azimuth (see the modules page for more information)
• Singlethreaded
• Environment variables set
  • PATH
  • AZIMUTH_HOME
  • AZIMUTH_EXAMPLES
• Example files in $AZIMUTH_EXAMPLES

Allocate an interactive session and run the program.
Sample session (user input in bold):

[user@biowulf]$ sinteractive
salloc.exe: Pending job allocation 46116226
salloc.exe: job 46116226 queued and waiting for resources
salloc.exe: job 46116226 has been allocated resources
salloc.exe: Granted job allocation 46116226
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3144 are ready for job

[user@cn3144 ~]$ module load Azimuth
[+] Loading Azimuth 2.0 ...
[user@cn3144 ~]$ python
Python 2.7.14 |Anaconda, Inc.| (default, Mar 27 2018, 17:29:31)
[GCC 7.2.0] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> import azimuth.model_comparison
>>> import numpy as np
>>> sequences = np.array(['ACAGCTGATCTCCAGATATGACCATGGGTT', 'CAGCTGATCTCCAGATATGACCATGGGTTT', 'CCAGAAGTTTGAGCCACAAACCCATGGTCA'])
>>> amino_acid_cut_positions = np.array([2, 2, 4])
>>> percent_peptides = np.array([0.18, 0.18, 0.35])
>>> predictions = azimuth.model_comparison.predict(sequences, amino_acid_cut_positions, percent_peptides)
No model file specified, using V3_model_full
>>> for i, prediction in enumerate(predictions):
...     print sequences[i], prediction
...
ACAGCTGATCTCCAGATATGACCATGGGTT 0.672298196907
CAGCTGATCTCCAGATATGACCATGGGTTT 0.687944237021
CCAGAAGTTTGAGCCACAAACCCATGGTCA 0.659245390401
>>> quit()

[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

Create a batch input file (e.g. Azimuth.sh). For example:

#!/bin/bash
module load Azimuth
python my_Azimuth.py

Submit this job using the Slurm sbatch command.

sbatch [--cpus-per-task=#] [--mem=#] Azimuth.sh

Create a swarmfile (e.g. Azimuth.swarm). For example:

python my_Azimuth.py
python my_Azimuth.py
python my_Azimuth.py
python my_Azimuth.py

Submit this job using the swarm command.

swarm -f Azimuth.swarm [-g #] [-t #] --module Azimuth