Ultra-fast kmer counter

UFKC is a high-performance kmer counter developed in Rust, designed to efficiently process both FASTA and FASTQ files using parallel processing.

Features

• Compatible with FASTA and FASTQ input files
• Supports gzipped files and automatic file-type identification
• In-built parallel processing for optimal performance on multi-core systems
• Offers the option to count reverse complement k-mers

Dependencies

• Rust programming language (version >= 1.54.0)
• clap (version >= 3.0.0)
• flate2 (version >= 1.0.20)
• rayon (version >= 1.5.1) Note: Dependencies will be automatically installed during compilation.

Installation

# Clone the repository
git clone https://github.com/pre-mRNA/UFKC.git

# Compile the code
cd UFKC && cargo build --release

# Add jank to your path
export PATH="$PATH:$(pwd)/target/release"

The compiled binary will be located in the target/release directory, and added to your current PATH.

Usage

UFKC [FLAGS] [OPTIONS] <input_file>

<input_file>: The input FASTA or FASTQ file (required)

Flags

-r, --count-reverse-complement: Count reverse complement k-mers as well

Options

-k, --kmer-size <k_value>: Size of k-mers to count (default: 9) -c, --cpu-count <cpu_count>: Number of CPU cores to use (default: 0, which means the program will use all available cores)

UFKC -k 7 -c 4 -r input.fasta

This command will count 7-mers in the input.fasta file, using 4 CPU cores, and also counting reverse complement k-mers.