Runs with Bisulfite sequencing data. It pre-processes raw data from FastQ inputs, aligns the reads and performs extensive quality-control on the results, using either Bismark or bwa-meth/MethylDackel.
Methyl-Seq is a bioinformatics best-practice analysis pipeline used for Methylation (BS-Seq) data analysis.
The pipeline uses Nextflow, a bioinformatics workflow tool. It pre-processes raw data from FastQ inputs, aligns the reads and performs extensive quality-control on the results. The pipeline allows you to choose between running either Bismark or bwa-meth / MethylDackel.
When we run analysis
We run this analysis routinely for all DNA-methylation projects where we have prepared the sequencing library in-house.
If you have prepared a library yourself and we are just sequencing, please get in touch and mention that you would like us to run this analysis.
The analysis works with any of the species that have a reference genome available in AWS-iGenomes. If in doubt, please ask whether we can run the pipeline for you.
bcl2fastq demultiplexed FastQ files and a genome reference.
The pipeline generates aligned BAM-files and gene count matrices, along with numerous quality control metrics. For more information, please see https://nf-co.re/methylseq/docs/output.