natir/kmrf

Kmer base Read Filter

kmrf 🧬 💻

kmrf (Kmer Ratio Filter), pronounced Amere Fine. Estimate read error rate with ratio .

• Instalation
• Usage
• Evaluation
• Minimum supported Rust version
• Citation

Instalation

If you haven't a rust environment you can use rustup or your package manager.

With cargo

Recommended solution.

cargo install --git https://github.com/natir/kmrf.git

With source

git clone https://github.com/natir/kmrf.git
cd kmrf
cargo install --path .

Usage

WIP

Evaluation

To plot against badread real error rate. You need badread reads in fasta format, pandas, altair package in your python environment and run this in kmrf directory:

cargo run --release -- -i {badread_reads.fasta} -o /dev/null -s {pcon_solid_kmer_file} -vvvv 2>&1 | grep "DEBUG" | cut -d$' ' -f 4 > {out.csv}
./script/real_error2ratio.py -i {out.csv} -f {badread_reads.fasta} -o out.{png|html}

Minimum supported Rust version

Currently the minimum supported Rust version is 1.57.0.

Citation

WIP