Search for LTR retrotransposons.
Project description
findltr
Command-line tool for de novo identification of LTR retrotransposons.
Requirements
Basic Local Alignment Search Tool (BLAST):
$ sudo apt-get install ncbi-blast+
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.
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