An algorithm for calculating flowtigs in a De Bruijn graph of DNA reads in metagenomes.
The input file should be an edgelist representing an arc-centric De Bruijn graph. The format of the edgelist should be as follows:
- Each edge is represented by a row with 4 values separated by a whitespace.
- The values, in this order, should be:
- Starting node
- Ending node
- Weight
- String sequence
The output of this algorithm is a FASTA file, which contains the safe maximal string sequences named by an index from 0 to <total number of sequences> - 1.
The algorithm is ran with the following command, assuming that Rust is installed:
cargo run --release -- -k {k} --input '{arc_centric_dbg}' --output '{safe_paths}' 2>&1 | tee -a '{log}'
where:
- {k} is the size of the k-mers used in the De Bruijn graph.
- {arc_centric_dbg} is the input edgelist.
- {safe_paths} is the desired path to the output file.
- {log} is the desired path to the log file.
The algorithm can also be ran without a log file with the following command:
cargo run --release -- -k {k} --input '{arc_centric_dbg}' --output '{safe_paths}'
First, install Rust if not yet installed.
Run the following code snippet in your terminal window
$ curl --proto '=https' --tlsv1.2 https://sh.rustup.rs -sSf | sh
Follow this link and follow the instructions to install rustup.
Create a new project with
cargo new hello_cargo <br>
cd hello_cargo
or navigate to your project directory, then run
cargo add flowtigs
or add flowtigs = "1.0.1" to your Cargo.toml file.