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.
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