Author: Kiki Cano-Gamez
Email: kiki.canogamez@well.ox.ac.uk
This repository contains a collection of codes to process sequencing data and modified based calling generated using Oxford Nanopore (ONT) sequencing.
The codes contained within this repository correspond to the main data processing steps followed. They are written in bash and ordered as follows:
./
|-- 0_merge-base-calls.sh Merges all base calls files (in BAM format) generated per barcode by the MinKNOW software into a single BAM file.
|-- 1_trim-adapters.sh Trims adapter and native barcode sequences from ONT reads using porechop.
|-- 2_align-reads.sh Aligns trimmed ONT reads to the genome using minimap2
|-- 3_repair-MM-rags.sh Repairs methylation information encoded in the MM tags of the aligned BAM file using modkit.
|-- 4_clip-reads.sh Removes methylation information from the end of reads (i.e. read clipping) using modkit.
|-- 5_get-methylation-calls.sh Recovers pileup at CpGs and quantifies 5mC and 5hmC events at each position of interest using modkit.
`-- get-mapping-statistics.sh Computes general mapping and alignment statistics from an aligned BAM file.