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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.



See versions of FragGeneScan which are available:

$ module avail fraggenescan

Load one version into your environment and run it:

$ module load fraggenescan/1.30
$ -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 '' -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
$ chmod 644 example/* train/* *.h *.c
$ sudo cp -r . /export/apps/fraggenescan/1.30
fraggenescan-software.txt · Last modified: 2020/03/15 09:17 by aorth