FragGeneScan is an application for finding (fragmented) genes in short reads. It can also be applied to predict prokaryotic genes in incomplete assemblies or complete genomes.

• Version: 1.30
• Added: July, 2015
• Updated: March, 2020
• Link: http://omics.informatics.indiana.edu/FragGeneScan/

See versions of FragGeneScan which are available:

$ module avail fraggenescan

Load one version into your environment and run it:

$ module load fraggenescan/1.30
./run_FragGeneScan.pl -genome=[seq_file_name] -out=[output_file_name] -complete=[1 or 0] -train=[train_file_name] -thread=[num_thread]

Note: Please remember to specify the same number of CPU threads as you have requested in your SBATCH job parameters.

Notes from the sysadmin during installation:

$ cd /tmp
$ wget 'https://downloads.sourceforge.net/project/fraggenescan/FragGeneScan1.30.tar.gz?r=https%3A%2F%2Fsourceforge.net%2Fprojects%2Ffraggenescan%2Ffiles%2FFragGeneScan1.30.tar.gz%2Fdownload&ts=1584261823' -O FragGeneScan1.30.tar.gz
$ tar xf FragGeneScan1.30.tar.gz 
$ cd FragGeneScan1.30
$ scl enable devtoolset-7 bash
$ make clean
$ make fgs
$ sudo mkdir -p /export/apps/fraggenescan/1.30
$ find . -perm /u+x -print -exec chmod  755 '{}' \;
$ sudo cp -r . /export/apps/fraggenescan/1.30