Unitig Flipper

This program takes in a set of unitigs as a FASTA file, and re-orients the unitigs heuristically in an attempt to minimize the number of dummy nodes in the SBWT of the k-mers.

Compiling

First, install the Rust. Then:

git submodule update --init
cargo build --release

This produces the binary to target/release/unitig_flipper. If you want to install the program to $PATH, run cargo install --path .

Usage

Usage: unitig_flipper --input <input> --output <output> -k <k>

Options:
  -i, --input <input>    Input FASTA or FASTQ file, possibly gzipped
  -o, --output <output>  Output FASTA or FASTQ file, possibly gzipped
  -k <k>                 k-mer length
  -h, --help             Print help