NanoTRF: software tool to de novo search high-copy tandem repeats in Oxford Nanopore Technologies (ONT) plant DNA sequencing data
Download the latest release:
wget https:/https://github.com/Kirovez/nanoTRF/releases/download/v1.0.0/nanoTRF-v1.0.0.tar.gz
tar -zxvf nanoTRF-v1.0.0.tar.gz && cd TideHunter-v1.0.0
Install via conda (recommended):
conda env create -f nanoTRF.yml
conda activate nanoTRF
(nanoTRF) python3 ./nanoTRF.py -r test.fasta -pTH -cu ./bin/canu -o./test/
or install all programs specified below and run data with special flags to specify the programs path:
- blastn and makeblastdb programs
- TideHunter programm
- Canu programm
- python >= v3.6
- python packages to be installed: biopython, networkx.
- java
conda env create -f nanoTRF.yml
conda activate nanoTRF
(nanoTRF) python3 ./nanoTRF.py -r test.fasta -pTH -cu ./bin/canu -o./test/
- Introduction
- Installation
- Getting Started
- Usage
- Commands and options
- Input
- Output
- Authors
- Acknowledgement
- License
NanoTRF is software tool to de novo search high-copy tandem repeats which is designed for raw long-read sequnces. It works with Oxford Nanopore Technologies (ONT) and Pacific Biosciences (PacBio) sequencing data.
On Linux/Unix, nanoTRF can be installed via creating an environment from an environment.yml file:
conda env create -f nanoTRF.yml
For running nanoTRF, please activate the conda environment:
conda activate nanoTRF
Your environment is ready to be used!
If you meet any issue with creating environment, please try the pre-built binary file:
wget https:/https://github.com/Kirovez/nanoTRF/releases/download/v1.0.0/nanoTRF-v1.0.0.tar.gz
tar -zxvf nanoTRF-v1.0.0.tar.gz && cd TideHunter-v1.0.0
Before you start, you need to make sure that all program and packages specified below is already installed on your computer. For running nanoTRF you will need to specify the programs path through special flags:
- blastn and makeblastdb programs. The paths to these programs can be set via -b and -mb flags, respectively
- TideHunter programm. It is recommended to download the latest release of TideHunter.The paths to these programs can be set via -pTH flags
- Canu programm. The latest release can be download here. The paths to these programs can be set via -cu flags
- java
- python >= v3.6
- python packages to be installed: biopython, networkx. To install these packages run the following command
pip install matplotlib biopython networkx python-louvain
or
pip3 install matplotlib biopython networkx python-louvain
Important note! If you have community python module installed you need to delete it because it interferes with python-louvain module used by nanoTRF. Use this command to delete community module:
pip3 uninstall community
To generate consensus sequences in FASTA format file (with usage default optional arguments):
python3 ./nanoTRF.py -r test.fasta -pTH -cu ./bin/canu -o./test/
To generate consensus sequences in FASTA format file, change number of theads that will be used and remove all unnecessary files and directories (with usage TideHunter files) using 30 threads:
python3 ./nanoTRF.py -r test.fasta --cu ./bin/canu -o ./test/ -th 30 -d -T TH.tab TH.out.fasta
Options:
General options:
-h --help show this help message and exit
Input:
-r --reads STR path to FastQ or Fasta file (required argument!!!)
-T --run_th STR path to output files of the TideHunter (if previously TideHunter was running by user):
table file with consensus sequnces and fasta file with uniq tandem repeats
Scoring parameters for partial order alignment:
-w --wordsize INT word size for wordfinder algorithm (length of best perfect match) [22]
-w_f --wordsize_f INT word size for wordfinder algorithm (length of best perfect match) in
the Reclusting module [15]
-ev --evalue INT expectation value (E) threshold for saving hits [2]
Clustering parameters:
-m --max_abundancy STR the proportion of amount lengths all tandem repeats in one cluster to length all the reads [0.0001]
-mOVe --min_Overlap STR the number of overlapping nucleotides between repeats in one cluster [10]
-ca --perc_abund STR minimum value of the TR cluster abundancy. ***Default = 0.009***
Path to programm for running nanoTRF:
-pTH --path_TH STR path to the location of TideHunter [TideHinter]
-cu --canu STR path to the location of Canu (required argument!!!It's missing in the conda)
-trf --TRF_run STR path to the location [trf]
-b --blast STR path to blastn executabled [blastn]
-mb --makedb STR path to makeblastdb executable [makeblastdb]
Output:
-o --out_directory STR path to work directory for output files where will be saved **(required argument!!!)
-lg --log_filepath STR path to file which list analysis parameters, modules and files,contains messages generated
in the various stages of the work [loging.log]
-nano --nano_trf STR fasta file with the TRs consensus sequences [nanoTRF.fasta]
-tab --nano_tab STR table file with the TRs abundancy [TR_info.tab]
Сomputational resources:
-th, --threads STR number of threads for running blast, canu. [4]
Additional option:
-d --dir_cleanup STR remove unncessary large files and directories from working directory [False]
-h, --help - show this help message and exit
NanoTRF works with FASTA and FASTQ formats.
NanoTRF generates output in tabular format:
| № | Column name | Description |
|---|---|---|
| 1 | Cluster | Name and cluster number |
| 2 | TRs length | Length of the TRs consensus sequence |
| 3 | Abundance |
NanoTRF generates TRs consensus sequences in FASTA format which contents information about TRs. The sequence descriptions have the following format:
>clustname monomer_length cluster_abund
clustname cluster number (for example: clust0)
monomer_length length of the TRs sequnce
cluster_abund cluster abundancy
Elizaveta Kolganova [email protected]
Ilya Kirov [email protected]
The project was financially supported by Russian Foundation for Basic Research (RFBR project № 17-00-00336)
This project is licensed under the MIT License