Basic Usage

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

ONT_logo

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

Common Use Cases

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

Notes and troubleshooting

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