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fibertools-rs

fibertools-rs a CLI tool for creating and interacting with fiberseq bam files.

Install

fibertools-rs is avalible through bioconda and can be installed with the following command: bash mamba install -c conda-forge -c bioconda fibertools-rs However, the bioconda version currently does not support GPU acceleration. If you would like to use GPU acceleration, you will need to install using the directions in the INSTALL.md file.

Usage

bash ft --help Help page for fibertools

Subcommands for fibertools-rs

ft predict-m6a

Predict m6A positions using HiFi kinetics data and encode the results in the MM and ML bam tags. Help page for predict-m6a.

ft add-nucleosomes

Add nucleosomes to a bam that file already contains m6a predictions. Note, this process is also run in the background during predict-m6a, so it is unnecessary to run independently unless you want to try new parameters for nucleosome calling. Help page for add-nucleosomes.

ft extract

Extracts fiberseq data from a bam file into plain text. Help page for extract.

ft extract --all

The extract all option is a special option that tries to extract all the fiberseq data into a tabular format. The following is an image of the output. Note that the column names will be preserved across different software versions (unless otherwise noted); however, the order may change and new columns may be added. Therefore, when loading the data (with pandas e.g.) be sure to use the column names as opposed to indexes for manipulation.

ft center

Center fiberseq reads (bam) around reference position(s). Help page for center.

Cite

Jha, A., Bohaczuk, S. C., Mao, Y., Ranchalis, J., Mallory, B. J., Min, A. T., Hamm, M. O., Swanson, E., Finkbeiner, C., Li, T., Whittington, D., Stergachis, A. B., & Vollger, M. R. (2023). Fibertools: fast and accurate DNA-m6A calling using single-molecule long-read sequencing. bioRxiv. https://doi.org/10.1101/2023.04.20.537673

Read the fibertools library docs

You can find the docs for the latest release here: https://docs.rs/fibertools-rs/latest/fibertools_rs/ or download from source and run: cargo doc --open and the docs will open in your browser.

TODO items

• [ ] Add a python API (see py-ft for progress)
• [ ] Use new iterator for ft extract and group writes to try and improve the speed
• [x] Set filters for ML depending on the model used
• [ ] long format extract command
• [ ] add option result to bamlift
• [ ] improve speed of liftover closest in bamlift. It takes about 50% of the time.
• [x] Add more test cases, learn about test modules in folders
• [x] GPU support
  • [ ] see if I can simplify or statically link PyTorch to get it onto bioconda
  • [ ] Detect GPU memory to set batch size dynamically.
• [ ] Improve progress bar for predict-m6a.
  • [ ] Get size of bam, say how far we are through the bam in terms of MB/GB?
• [ ] Add unaligned, secondary, supplemental reads to the test bam.