a tool for designing crispr libraries
install blast
```
sudo apt-get install ncbi-blast+
```
the above installs in an outdated version on ubuntu 14.04, which is buggy
```
$ blastn -version
blastn: 2.2.28+
Package: blast 2.2.28, build Jun 3 2013 11:17:14
```
do this instead:
```
conda install -c https://conda.anaconda.org/bioconda blast
```
actually no, it is not working either! so do this instead:
```
$ wget ftp://ftp.ncbi.nlm.nih.gov/blast/executables/LATEST/ncbi-blast-2.3.0+-x64-linux.tar.gz
$ tar xvfp ncbi-blast-2.3.0+-x64-linux.tar.gz
$ export PATH=”$PATH:$HOME/ncbi-blast-2.2.29+/bin”
$ mkdir ./ncbi-blast-2.2.29+/db
$export BLASTDB=”$HOME/ncbi-blast-2.2.29+/db”
```
results in a version of ncbi which supports -max_hsps (previously -max_hsps_per_target was buggy)
```
$ blastn -version
blastn: 2.2.31+
Package: blast 2.2.31, build Dec 3 2015 17:28:17
```
genral cli tools
```
sudo apt-get install tree
sudo apt-get install jq
```
bioinformatics tools
```
sudo apt-get install bedtools
sudo apt-get install tabix
sudo apt-get install igv
```
this software
```
pip install git+https://github.com/alaindomissy/buffet.git#egg=pycrispr
```
primer3 dependency is not yet included in the setup.py config, and needs to be pip installed separately
```
pip install primer3-py
```
pycrispr runs on Python 2.7, 3.3 and 3.4
Given a genomic interval, and a rference genome, obtain all candidate crispr guides, resulting from enzymatic digestion via cripsr-eating protocol
```
enzymatic_protospacers(
'~/scaffolds_directory/',
'chr6:136640001-136680000',
'mm8.fasta'
)
```
Score candidates, define and rank by yield of good guides all possible clusters of consecutive good guides
```
high_specificity_clusters(
scaffolds_directory,
genomic_coord, reference,
genome
)
```
Advanced options:
```
minimum_specificity_clusters(
scaffolds_directory, genomic_coord, reference, genome,
chunk_size=25,
max_hsps=25,
ref_substrate_id='chr6',
low=75,
high=75,
load_genome=False,
howmany=None
)
```
Given a required number of guides, design amplification primers for enough top-yielding good-guides clusters
```
primer_design(scaffolds_directory, genomic_coord, reference, genome, required_number_of_guides)
```