Identify and annotate mutations from genome editing assays.

Overview

CRISPR-detector

Here we propose our CRISPR-detector to facilitate the CRISPR-edited amplicon and whole genome sequencing data analysis, with functions that existing tools are not able to provide.

CRISPR-detector brings the following four key innovations :

  1. optimized processing time allowing for hundreds of amplicons or whole genome sequencing data;
  2. integrated structural variation calling;
  3. edited and control sample co-analysis, to remove background variants not induced by gene-editing;
  4. functional and clinical consequences annotation of editing-induced mutations.

System requirements

Sentieon module

Download sentieon toolkit from https://s3.amazonaws.com/sentieon-release/software/sentieon-genomics-202010.03.tar.gz
You may request a license by sending emails to [email protected]

export SENTIEON_LICENSE=PATH_TO_SENTIEON/sentieon-genomics-202010.03/localhost_eval.lic
export PATH=PATH_TO_SENTIEON/sentieon-genomics-202010.03/bin:$PATH

Python packages

pip install biopython
pip install pyfaidx
pip install -U textwrap3
conda install blast
conda install samtools

ANNOVAR

Download ANNOVAR from https://www.openbioinformatics.org/annovar/annovar_download_form.php

perl annotate_variation.pl -downdb -webfrom annovar avdblist humandb/ -buildver hg38
perl annotate_variation.pl -buildver hg38 -downdb -webfrom annovar refGene humandb/
perl annotate_variation.pl -buildver hg38 -downdb -webfrom annovar clinvar_20210501 humandb/
export PATH=PATH_TO_ANNOVAR/annovar:$PATH

Organism Homo sapiens Experiment type sequencing data support variant annotations from refGene & ClinVar, other species may only support refGene annotations

Usage

1. Single amplicon & pooled amplicons sequencing data analysis

python CRISPRdetectorCORE.py
--sample, sample name & output dir
--e1, treated group fq1 path, required = True
--e2, treated group fq2 path, required = False
--c1, control group fq2 path, required = False
--c2, control group fq2 path, required = False
--ref_fasta, single or pooled amplicon(s) sequence(s) path in fasta format, required=True
--threads, number of threads to run sentieon minimap2 & driver module, default=1
--anno, annotate variants with ANNOVAR [1] or not run ANNOVAR [2], required=False
--assembly, path to assembly in fasta format : hg38.fa mm9.fa ... required=False
--species, species : Homo_sapiens,Mus_musculus... required=False
--db, ANNOVAR database path, required=False

2. Whole genome sequencing (WGS) data analysis

python CRISPRdetectorWGS.py
--e1, treated group fq1 path, required = True
--e2, treated group fq2 path, required = False
--c1, control group fq2 path, required = False
--c2, control group fq2 path, required = False
--sample, sample name & output dir
--threads, number of threads to run sentieon minimap2 & driver module, default=1
--bed, bed format file input to call variants of interest region, required=False
--anno, annotate variants with ANNOVAR [1] or not run ANNOVAR [2], required=False
--assembly, path to assembly in fasta format : hg38.fa mm9.fa ... required=False
--species, species : Homo_sapiens,Mus_musculus... required=False
--db, ANNOVAR database path, required=False

Owner
hlcas
hlcas
Multiple GNOME terminals in one window

Terminator by Chris Jones [email protected] and others. Description Terminator was

GNOME Terminator 1.5k Jan 01, 2023
Change your Windows background with this program safely & easily!

Background_Changer Table of Contents: About the Program Features Requirements Preview Credits Reach Me See Also About the Program: You can change your

Sina.f 0 Jul 14, 2022
Subcert is an subdomain enumeration tool, that finds all the subdomains from certificate transparency logs.

Subcert Subcert is a subdomain enumeration tool, that finds all the valid subdomains from certificate transparency logs. Table of contents Setup Demo

A3h1nt 59 Dec 16, 2022
Fast STL (ASCII & Binary) importer for Blender

blender-fast-stl-importer Fast STL (ASCII & Binary) importer for Blender based on https://en.wikipedia.org/wiki/STL_(file_format) Technical notes: flo

Iyad Ahmed 7 Apr 17, 2022
Datargsing is a data management and manipulation Python library

Datargsing What is It? Datargsing is a data management and manipulation Python library which is currently in deving Why this library is good? This Pyt

CHOSSY Lucas 10 Oct 24, 2022
A middle-to-high level algorithm book designed with coding interview at heart!

Hands-on Algorithmic Problem Solving A one-stop coding interview prep book! About this book In short, this is a middle-to-high level algorithm book de

Li Yin 1.8k Jan 02, 2023
Cairo hooks for pre-commit

pre-commit-cairo Cairo hooks for pre-commit. See pre-commit for more details Using pre-commit-cairo with pre-commit Add this to your .pre-commit-confi

Fran Algaba 16 Sep 21, 2022
Simple AoC helper program you can use to develop your own solutions in python.

AoC-Compabion Simple AoC helper program you can use to develop your own solutions in python. Simply install it in your python environment using pip fr

Alexander Vollmer 1 Dec 20, 2021
Generate Azure Blob Storage account authentication headers for Munki

Azure Blob Storage Authentication for Munki The Azure Blob Storage Middleware allows munki clients to connect securely, and directly to a munki repo h

Oliver Kieselbach 10 Apr 12, 2022
Cairo-bloom - A naive bloom filter implementation in Cairo

🥀 cairo-bloom A naive bloom filter implementation in Cairo. A Bloom filter is a

Sam Barnes 37 Oct 01, 2022
Syarat.ID Source Code - Syarat.ID is a content aggregator website

Syarat.ID is a content aggregator website that gathering all informations with the specific keyword: "syarat" from the internet.

Syarat.ID 2 Oct 15, 2021
A python script to turn tabs into spaces the right way.

detab A python script to turn tabs into spaces the right way. detab turns all tabs into spaces, not just leading tabs. Not all tabs have the same leng

1 Jan 26, 2022
Projects using the Tkinter module in Python!

Tkinter projects This repository includes some Tkinter projects made by me. All of these are simple to understand. I create apps with good functionali

Amey 0 Sep 24, 2021
Script de monitoramento de telemetria para missões espaciais, cansat e foguetemodelismo.

Aeroespace_GroundStation Script de monitoramento de telemetria para missões espaciais, cansat e foguetemodelismo. Imagem 1 - Dashboard realizando moni

Vinícius Azevedo 5 Nov 27, 2022
A collection of simple tools that proved to be needed for hadling large periodic calculations with the VASP software package.

VESTA-tools A collection of simple tools that proved to be needed for handling large periodic calculations with the VASP software package. distTotCalc

Ilia Kichev 2 Dec 14, 2021
Something like Asteroids but not really, done in CircuitPython

CircuitPython Staroids Something like Asteroids, done in CircuitPython. Works with FunHouse, MacroPad, Pybadge, EdgeBadge, CLUE, and Pygamer. circuitp

Tod E. Kurt 14 May 31, 2022
Simple module with some functions such as generate password (get_random_string)

Simple module with some functions such as generate password (get_random_string), fix unicode strings, size converter, dynamic console, read/write speed checker, etc.

Dmitry 2 Dec 03, 2022
[arXiv 2020] Video Representation Learning with Visual Tempo Consistency

Video Representation Learning with Visual Tempo Consistency [Paper] [Project Page] News Full codebae is coming soon Pretained Models For now, we provi

DeciForce: Crossroads of Machine Perception and Autonomy 24 Nov 23, 2022
A module comment generator for python

Module Comment Generator The comment style is as a tribute to the comment from the RA . The comment generator can parse the ast tree from the python s

飘尘 1 Oct 21, 2021
A simple program to run through inputs for a 3n+1 problem

Author Tyler Windemuth Collatz_Conjecture A simple program to run through inputs for a 3n+1 problem Purpose: doesn't really have a purpose, did this t

0 Apr 22, 2022