dragmap-meth: Fast and accurate aligner for bisulfite sequencing reads using dragmap

Overview

dragmap_meth (dragmap_meth.py)

Alignment of BS-Seq reads using dragmap.

Intro

This works for single-end reads and for paired-end reads from the directional protocol (most common).

Installation

Install dragmap-meth via pip

dragmap-meth is available on https://pypi.org/project/dragmap-meth/

pip install dragmap-meth

Install dragmap-meth via conda

conda env create -n env4dragmap-meth --file environment.yaml python=3
https://github.com/xie186/dragmap-meth.git

python ./dragmap-meth.py -h 
usage: dragmap-meth.py [-h] {buildhashtable,dragmap} ...

dragmap-meth: bisulfite reads mapper using dragmap-meth

positional arguments:
  {buildhashtable,dragmap}
                        sub-command help
    buildhashtable      Build hash table of a reference genome for alignent
    dragmap             Align bisulfite reads using dragmap

options:
  -h, --help            show this help message and exit

QuickStart

The commands:

python dragmap-meth.py buildhashtable -r ref.fa -o ref/
python  dragmap-meth.py dragmap -ht ref/ -r1 t_R1.fastq.gz -r2 t_R2.fastq.gz |samtools view -bS - -o dragmap-meth.bam

will create dragmap-meth.bam. To align single end-reads, specify only 1 file: -r1 some_read.fastq.gz

Dependencies

Python 3.10.1
dragmap

Reference:

Introducing DRAGMAP, the new genome mapper in DRAGEN-GATK: https://gatk.broadinstitute.org/hc/en-us/articles/4410953761563-Introducing-DRAGMAP-the-new-genome-mapper-in-DRAGEN-GATK

Demystifying the versions of GRCh38/hg38 Reference Genomes, how they are used in DRAGEN™ and their impact on accuracy: https://www.illumina.com/science/genomics-research/articles/dragen-demystifying-reference-genomes.html

https://github.com/DavidStreid/bio_docker/tree/main/dragmap

https://github.com/HudsonAlpha/CSL_public_benchmark

Acknowledgement

Special thanks to bwa-meth. Part of the codes were adapted from bwa-meth.

Owner
Shaojun Xie
Bioinformatics Core Assistant Director @ Purdue University
Shaojun Xie
Blender addons - A collection of Blender tools I've written for myself over the years.

gret A collection of Blender tools I've written for myself over the years. I use these daily so they should be bug-free, mostly. Feel free to take and

217 Jan 08, 2023
YunoHost is an operating system aiming to simplify as much as possible the administration of a server.

YunoHost is an operating system aiming to simplify as much as possible the administration of a server. This repository corresponds to the core code, written mostly in Python and Bash.

YunoHost 1.5k Jan 09, 2023
Add all JuliaLang unicode abbreviations to AutoKey.

Autokey Unicode characters Usage This script adds all the unicode character abbreviations supported by Julia to autokey. However, instead of [TAB], th

Randolf Scholz 49 Dec 02, 2022
The presented desktop application was made to solve 1d schrodinger eqation

schrodinger_equation_1d_solver The presented desktop application was made to solve 1d schrodinger eqation. It implements Numerov's algorithm (step by

Artem Kashapov 2 Dec 29, 2021
DRF magic links

drf-magic-links Installation pip install drf-magic-links Add URL patterns # urls.py

Dmitry Kalinin 1 Nov 07, 2021
Personal Chat Assistance

Python-Programming Personal Chat Assistance {% import "bootstrap/wtf.html" as wtf %} titleEVT/title script src="https://code.jquery.com/jquery-3.

PRASH_SMVIT 2 Nov 14, 2021
Extended functionality for Namebase past their web UI

Namebase Extended Extended functionality for Namebase past their web UI.

RunDavidMC 12 Sep 02, 2022
Certipy is a Python tool to enumerate and abuse misconfigurations in Active Directory Certificate Services (AD CS).

Certipy Certipy is a Python tool to enumerate and abuse misconfigurations in Active Directory Certificate Services (AD CS). Based on the C# variant Ce

ollypwn 1.3k Jan 01, 2023
Script to automate the scanning of "old printed photos"

photoscanner Script to automate the scanning of "old printed photos" Just run: ./scan_photos.py The script is prepared to be run by fades. Otherw

Facundo Batista 2 Jan 21, 2022
A dashboard for your code. A build system.

NOTICE: THIS REPO IS NO LONGER UPDATED Changes Changes is a build coordinator and reporting solution written in Python. The project is primarily built

Dropbox 763 Sep 09, 2022
Discovering local read-level DNA methylation patterns and DNA methylation heterogeneity in intermediately methylated regions

Discovering local read-level DNA methylation patterns and DNA methylation heterogeneity in intermediately methylated regions

1 Jan 11, 2022
Zeus is an open source flight intellingence tool which supports more than 13,000+ airlines and 250+ countries.

Zeus Zeus is an open source flight intellingence tool which supports more than 13,000+ airlines and 250+ countries. Any flight worldwide, at your fing

DeVickey 1 Oct 22, 2021
Automatización del proceso Inmofianza

Selenium Inmofianza Proyecto de pruebas automatizadas con selenium webdriver para el aplicativo Omnicanalidad Pre-requisitos 📋 Componentes que deben

Natalia Narváez 1 Jan 07, 2022
CountBoard 是一个基于Tkinter简单的,开源的桌面日程倒计时应用。

CountBoard 是一个基于Tkinter简单的,开源的桌面日程倒计时应用。 基本功能 置顶功能 是否使窗体一直保持在最上面。 简洁模式 简洁模式使窗体更加简洁。 此模式下不可调整大小,请提前在普通模式下调整大小。 设置功能 修改主窗体背景颜色,修改计时模式。 透明设置 调整窗体的透明度。 修改

gaoyongxian 130 Dec 01, 2022
Show my read on kindle this year

Show my kindle status on GitHub

yihong 26 Jun 20, 2022
This is an online course where you can learn and master the skill of low-level performance analysis and tuning.

Performance Ninja Class This is an online course where you can learn to find and fix low-level performance issues, for example CPU cache misses and br

Denis Bakhvalov 1.2k Dec 30, 2022
Grimoire is a Python library for creating interactive fiction as hyperlinked html.

Grimoire Grimoire is a Python library for creating interactive fiction as hyperlinked html. Installation pip install grimoire-if Usage Check out the

Scott Russell 5 Oct 11, 2022
Linux Security and Monitoring Scripts

Linux Security and Monitoring Scripts These are a collection of security and monitoring scripts you can use to monitor your Linux installation for sec

Andre Pawlowski 65 Aug 27, 2022
Gmvault: Backup and restore your gmail account

Gmvault: Backup and restore your gmail account Gmvault is a tool for backing up your gmail account and never lose email correspondence. Gmvault is ope

Guillaume Aubert 3.5k Jan 01, 2023
Solutions for the Advent of Code 2021 event.

About 📋 This repository holds all of the solution code for the Advent of Code 2021 event. All solutions are done in Python 3.9.9 and done in non-real

robert yin 0 Mar 21, 2022