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FragGeneScan++

A modified fork of FragGeneScan-Plus.

This tool is no longer maintained. It was replaced by FragGeneScanRs, a drop-in replacement for FragGeneScan, implemented in rust. FragGeneScanRs is both faster and contains a number of bug fixes that are present in both FragGeneScan and FragGeneScanPlusPlus.

Installation

The installation instruction from FGS+ remain valid:

  1. Install make and gcc.

  2. Clone this repository and go to the repository root.

    git clone https://github.com/unipept/FragGeneScanPlusPlus.git
cd FragGeneScanPlusPlus

  3. Run make.

Running

An example usage of FragGeneScan++ looks like the following:

./FGSpp -s example/NC_000913-454.fna -o output -w 0 -t 454_5 -p 16

If you're running FGSpp from outside the repo, supply the training directory location with -r:

FGSpp -s <this-repo>/example/NC_000913-454.fna -o output -w 0 -r <this-repo>/train -t 454_5 -p 16

For more info or a list of all options, run FragGeneScan++ without arguments.

Output files

Upon completion, FragGeneScan++ can generate 3 files:

  • The [output_file].faa file lists amino acid sequences in FASTA format corresponding to the putative genes. The [output_file].faa file is always generated.
  • The [output_file].ffn file lists the nucleotide sequences in FASTA format corresponding to the putative genes. This file is not automatically generated: to obtain this file, set the -d flag to 1.
  • The [output_file].out file lists the coordinates of putative genes. This file consists of 5 columns ( start position, end position, strand, frame, and score). This file is not automatically generated: to obtain this file, set the -e flag to 1.

License

FragGeneScan++ is released under under the terms of the GNU General Public License, version 3 (or any later version), as published by the Free Software Foundation.

Please see the LICENSE file for further information.