This repository contains tools and data related to Enzymatic Methylation Sequencing and Enzymatic 5hmC-seq (E5hmC-seq)
There are 3 nextflow scripts:
Reference genomes containing spike-in methylation controls are available via an amazon s3 bucket: s3://neb-em-seq-sra/
To use the Nextflow v1 scripts in this repository you need an older version of nextflow.
NXF_VER=22.10.4 nextflow run em-seq.nf --genome em-seq_ref_files/T2T_chm13v2.0+bs_controls.fa --flowcell AAC27FDF --fastq_glob '*_R{1,2}.fastq*' -resume
We hope to upgrade to the NextFlow v2 syntax in the future.
You may also be interested in the nf-core methylseq project