continuous-methylation

A bioinformatics pipeline to get methylation calls (in bed format) for phased alignments using long-read sequencing (third-gen) data.

This pipeline accepts only hifi OR ont, and it can 1) generate phased alignments using a phased assembly if parental illuminas are available, 2) generate phased alignments using heterozygous SNVs + SVs and will output a single bam that you can query using "HP:i:1 or HP:i:2 or ![HP]" to get the phased reads.

Getting started

1. Clone the repo
2. Install Snakemake version >= 7.6.0
3. Fill in the config and manifests.
4. Start the analysis!
   • Begin with a dry-run

   ./runlocal 10 -np
   

   • If dry-run looks good, proceed with:

   ./runlocal 10
   

To-do

• Put in CI tests
• Add conda enviroments
• Build bare-bone container to get minimal example running
• Further chunk the alignment files (beyond chromosomes) in case these files are astronomical (non-human primates)

FAQ

1. What if I want to change the version of certain tools?
   1. You could change the defaults in the tools.yaml config, and if you want to change the resources needed for certain steps- then please refer to the snakemake documentation regarding this topic

   ./config
   ├── config.yaml
   ├── manifest.tab
   └── tools.yaml
   

2. How do I use different tech?
   1. Currently, there is only support for hifi or ont. You could use the pipeline like the following:

   # ONT
   ./runsnake 30 --config tech=ont manifest=config/manifest.tab (for dry run: put -np)
    
   # HiFi
   ./runsnake 30 --config tech=hifi manifest=config/manifest-hifi.tab (for dry run: put -np)
   

3. How do I know if I have methylation tags in my unmapped bam? Assuming you have samtools installed:

samtools view -e '[MM]' your_bam_here.bam

4. Where can I get the singularity containers?
   1. Answer coming soon. I'm going to build a barebone container that is enough to run the pipeline, as well as adding a conda statement for all the rules so it can be fine tuned on the versioning.
5. What is an example config and manifest?
   1. Answer coming soon.

Overview

DAG for HiFi DAG for ONT