Skip to content

Latest commit

 

History

History
86 lines (61 loc) · 3.45 KB

README.md

File metadata and controls

86 lines (61 loc) · 3.45 KB
Raw

Flowtigs

An algorithm for computing flowtigs from DNA reads of a metagenome.

The steps to compute flowtigs from reads are the following:

  1. Install Rust
  2. Run ggcat or bcalm on the reads
  3. Run flowtigs on the output of ggcat or bcalm

1. Installation of Rust

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.

2. Running ggcat

ggcat takes reads as input and outputs a file that can be used by flowtigs, see example of the input and output format of ggcat. Download ggcat with the following commands

git clone https://github.com/algbio/ggcat --recursive
cd ggcat/
git checkout a91ecc97f286b737b37195c0a86f0e11ad6bfc3b
cargo update time
cargo install --path crates/cmdline/ --locked --features "kmer-counters"

Then, ggcat is run with

ggcat build -k <k> -j <threads> -e -s <minimum multiplicity> '<input file name>' -o '<output file name>'

where

  • <k> represents the desired k-value, which is the same that will be used by flowtigs
  • <threads> represents the number of threads on which ggcat will run
  • <minimum multiplicity> minimum multiplicity needed for a k-mer to occur
  • <input file> represents the path to the input file which contains the reads
  • <output file> represents the path to the desired output file, which will be the input file for flowtigs

If you get the error message Command 'ggcat' not found, either add $HOME/.cargo/bin to your $PATH variable, or run ggcat with the following command intead.

~/.cargo/bin/ggcat build -k <k> -j <threads> -e -s <minimum multiplicity> '<input file name>' -o '<output file name>'

3. Running flowtigs

The input of flowtigs should be a file in the same format as the output of bcalm or ggcat. An example can be seen here.

Clone this project with the following commands

git clone https://github.com/elieling/flowtigs.git
cd flowtigs
cargo install --path . --locked

Then, run flowtigs with the folowing code in the project directory

flowtigs --input "<input file>" -k <k> -t <threshold> --output "<output file>"

where

  • <input file> represents the path to the input file
  • <k> represents the desired k-value
  • <threshold> represents the desired threshold for filtering. To run flowtigs without filtering, use threshold 0
  • <output file> represents the path to the desired output file

If you get the error message Command 'flowtigs' not found, either add $HOME/.cargo/bin to your $PATH variable, or run flowtigs with the following command intead.

~/.cargo/bin/flowtigs --input "<input file>" -k <k> -t <threshold> --output "<output file>"

Output

The output of flowtigs is a FASTA file, which contains the safe maximal string sequences named by an index from 0 to <total number of sequences> - 1. See example here.