fibertools-rs

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

Install

Installation from cargo requires a recent version of gcc and cmake. I have tested and recommend these versions of gcc and cmake, though other versions may work:

module load gcc/10.2.0 cmake/3.21.1

From (recommended)

cargo install fibertools-rs

How to install cargo.

Install with support for CNN m6A prediction

cargo install fibertools-rs --features cnn

From (latest version not always available)

mamba install -c conda-forge -c bioconda fibertools-rs

From github (active development)

cargo install --git https://github.com/mrvollger/fibertools-rs

fibertools-rs

Help page for fibertools

ft extract

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

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

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

ft-predict-m6a

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

TODO

• Add rustybam stats to ft all
• Add CNN to CI
• Option to keep full float info in predict-m6a
• Add option for all format but without sequence
• handle broken pipe errors in ft-extract
• add rq to all