findltr

Command-line tool for de novo identification of LTR retrotransposons.

Requirements

• Basic Local Alignment Search Tool (BLAST):

  $ sudo apt-get install ncbi-blast+
  

• Genome Tools(GT) with enabled HMMER option(with-hmmer=yes) via compilation.

Installations

Example install, using VirtualEnv:

# install/use python virtual environment
virtualenv ~/virtenv_scratch --no-site-packages

# activate the virtual environment
source ~/virtenv_scratch/bin/activate

# upgrade pip in the new virtenv
pip install -U pip setuptools

# install this package in DEVELOPMENT mode
python setup.py develop

# or simply install
# python setup.py install

Options

The list of available options:

General

--input	Input *.fasta or *.fa file
--output	Output *.gff file

Search parameters

Option	Description	Default
--algorithm	Algorithm, [kmp|salcp|original]	original
--pattern_len	Length of pattern	20
--min_distance	Minimal distance between LTRs	1000
--max_distance	Maximal distance between LTRs	20000
--min_ltr_len	Minimal length of LTRs	100
--max_ltr_len	Maximal length of LTRs	1000

Other

--verbose	Include more details
--debug	Turn on debugging output, do not catch exceptions

See findltr --help for complete list of available options.