Flowtigs

An algorithm for calculating flowtigs in a De Bruijn graph of DNA reads in metagenomes.

Input

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:
  1. Starting node
  2. Ending node
  3. Weight
  4. String sequence

Output

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.

Running instructions

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}'

Installation

First, install Rust if not yet installed.

Installing Rust on Linux or macOS

Run the following code snippet in your terminal window

$ curl --proto '=https' --tlsv1.2 https://sh.rustup.rs -sSf | sh

Installing Rust on Windows

Follow this link and follow the instructions to install rustup.

Installing flowtigs

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.