align

Description

In the preprocessing and alignment of DNA methylation data, the combination of Fastp and BWA-MEM provides a robust and efficient solution. Fastp ensures the removal of low-quality reads and adapter contamination, thereby enhancing the overall data quality.

Following preprocessing with Fastp, the cleaned data is then subjected to alignment using BWA-MEM, a widely used aligner for mapping sequencing reads to a reference genome. The aligned data serves as a crucial foundation for downstream analyses, enabling the identification of methylated regions and providing insights into the epigenetic landscape.

Usage

An example usage is:
    dmtools align --fastp fastp -g genome.fa -1 te1.fq -2 te2.fq -g genome.fa -o meth.bam

Important

genome.fa should be indexed with dmtools index -g genome.fa.

Important

if --fastp is not defined, the input file should be clean data.

Paramaters

[ Main paramaters ]
--genome/-g	Name of the genome mapped against, MUST build index first dmtools index
-i	input file, support .fq/.fastq and .gz/.gzip format.
-1	input file left end, if single-end. please use -i
-2	input file right end
-o	Prefix of BAM output file
--fastp	fastp program location for fastq preprocess.
-p	[int] threads
--help/-h	Print help

Tip

For feature requests or bug reports please open an issue on github.