https://github.com/xie186/dragmap-meth
dragmap-meth: Fast and accurate aligner for bisulfite sequencing reads using dragmap
https://github.com/xie186/dragmap-meth
bs-seq dragmap
Last synced: 5 months ago
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dragmap-meth: Fast and accurate aligner for bisulfite sequencing reads using dragmap
- Host: GitHub
- URL: https://github.com/xie186/dragmap-meth
- Owner: xie186
- License: mit
- Archived: true
- Created: 2021-12-17T15:43:35.000Z (over 4 years ago)
- Default Branch: master
- Last Pushed: 2022-01-13T22:27:05.000Z (over 4 years ago)
- Last Synced: 2025-07-11T18:46:45.688Z (11 months ago)
- Topics: bs-seq, dragmap
- Language: Python
- Homepage: https://github.com/xie186/dragmap-meth
- Size: 13.7 MB
- Stars: 3
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# dragmap_meth (dragmap_meth.py)
Alignment of BS-Seq reads using [dragmap](https://github.com/Illumina/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
git clone https://github.com/xie186/dragmap-meth.git
cd dragmap-meth/
```
## 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](https://github.com/brentp/bwa-meth). Part of the codes were adapted from bwa-meth.