nested (now also called TE-greedy) is software to analyze nested LTR transposable elements in DNA sequences, such as reference genomes. It is made of two components: nested-generator for generating simulated sequences of nested retrotransposons, and nested-nester (now called TE-greedy-nester) that looks for nested, as well as non-nested and solo-LTR repeat sequences in the input. Unlike other similar software, TE-greedy-nester is structure-based by using de-novo retrotransposon identification software LTR Finder, relying on sequence information only secondarily.

References:

• Matej Lexa, Pavel Jedlicka, Ivan Vanat, Michal Cervenansky, Eduard Kejnovsky TE-greedy-nester: structure-based detection of LTR retrotransposons and their nesting Bioinformatics, Volume 36, Issue 20, October 2020, Pages 4991–4999

• Nested Main Site

• Module Name: nested (see the modules page for more information)
• Example files in /usr/local/apps/nested/2.0.0/test_data

Allocate an interactive session and run the program.
Sample session (user input in bold):

[user@biowulf]$ sinteractive
salloc.exe: Pending job allocation 46116226
salloc.exe: job 46116226 queued and waiting for resources
salloc.exe: job 46116226 has been allocated resources
salloc.exe: Granted job allocation 46116226
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3144 are ready for job

[user@cn3144 ~]$ module load nested
[+] Loading nested  2.0.0  on cn3144
[+] Loading singularity  3.10.5  on cn3144

[user@cn3144 ~]$nested-nester --help
Usage: nested-nester [OPTIONS] INPUT_FASTA

Options:
  -s, --sketch                    Sketch output.
  -f, --format TEXT               Format for GFF.
  -o, --output_fasta_offset INTEGER
                                  Number of bases around the element included
                                  in output fasta files.
  -d, --output_folder PATH        Output data folder.
  -t, --initial_threshold INTEGER
                                  Initial threshold value.
  -m, --threshold_multiplier FLOAT
                                  Threshold multiplier.
  -n, --threads INTEGER           Number of threads
  -dt, --discovery_tool [LTR_finder|LTRharvest|finder|harvest]
                                  Determines which tool is used for
                                  retrotransoson discovery. Default:
                                  LTR_finder
  -solo, --solo_ltrs              Run solo LTR module
  --help                          Show this message and exit.

[user@cn3144 ~]$ nested-generator --help
Usage: nested-generator [OPTIONS] INPUT_DB OUTPUT_DB

Options:
  -l, --baselength INTEGER        Baselength for generated elements.
  -i, --number_of_iterations INTEGER
                                  Number of inserted elements.
  -n, --number_of_elements INTEGER
                                  Number of generated sequences.
  -f, --filter                    Filter database and create new one with
                                  given output db path.
  -s, --filter_string TEXT        Filter entries by given string [ONLY
                                  RELEVANT WITH -filter OPTION].
  -o, --filter_offset INTEGER     LTR offset allowed [ONLY RELEVANT WITH
                                  -filter OPTION].
  -p, --percentage INTEGER        Percentage of elements in generated
                                  sequence.
  -a, --average_element INTEGER   Average element length in database.
  -e, --expected_length INTEGER   Expected output sequence length [ONLY WORKS
                                  WITH -percentage and -average_element].
  -d, --output_directory TEXT     Output directory.
  --help                          Show this message and exit.

Example running nested

[user@cn3144 ~]$cp -a /usr/local/apps/nested/2.0.0/test_data/ . 
[user@cn3144 ~]$ nested-nester test_data/151kb_adh1_bothPrimes.fasta
/usr/local/lib/python3.9/dist-packages/nested-1.0.0-py3.9.egg/nested/config/config.py:14: YAMLLoadWarning: calling yaml.load() without Loader=... is deprecated, as the default Loader is unsafe. Please read https://msg.pyyaml.org/load for full details.
Processing adh1_vicinity_150bpPlMin
Processing adh1_vicinity_150bpPlMin: DONE [0:00:10.348563]
Total time: 0:00:10.350736
Number of errors: 0

For more information please see the GitLab Page