Basic Usage

modkit is a bioinformatics tool for working with modified bases from Oxford Nanopore.

Installation

Pre-compiled binaries are provided for Linux from the release page. We recommend the use of these in most circumstances. As a rust-based project, modkit can also be installed with cargo.

git clone https://github.com/nanoporetech/modkit.git
cd modkit
cargo install --path modkit
# or
cargo install --git https://github.com/nanoporetech/modkit.git

Common Use Cases

1. Creating a bedMethyl table with pileup
2. Summarizing a modBAM with modbam summary
3. Extracting per-read base modification data into a table
4. Checking modified base tags in a modBAM
5. Making a motif BED file with motif-bed
6. Performing differential methylation scoring with dmr
7. Convert bedMethyl files to bigWig for visualization
8. Predict regions of open chromatin on MTase-treated DNA
9. Updating and Adjusting MM tags with adjust-mods and update-tags
10. Convert modification probabilities into hard calls
11. Removing base modification calls at the ends of reads
12. Narrow analysis to only specific positions with a BED file
13. Repairing/adding MM/ML tags to reads with clipped sequences
14. Creating hemi-methylation pattern bedMethyl tables with pileup-hemi

Notes and troubleshooting

1. General troubleshooting
2. Threshold evaluation examples (for advanced users)
3. Querying the logs in motif search