NESTED on Biowulf

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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

Documentation

Nested Main Site

Important Notes

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

Getting Started

Interactive jobs should be used for debugging, graphics, or applications that cannot be run as batch jobs.

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

Most jobs should be run as batch jobs.

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