Introduction

T2Tools is a toolset contains several tools for T2T assembly, and it is under development.

Dependencies

Software

• Python (>=3.7)
• TRF (Tandem Repeat Finder)

Python Modules

• matplotlib
• numpy
• pathos

Installation

Add TRF to your environment variable PATH

cd /path/to/install
git clone https://github.com/sc-zhang/T2Tools.git
pip install -r requirements.txt
chmod +x T2Tools/t2tools.py
echo 'export PATH=/path/to/install/T2Tools:$PATH' >> ~/.bash_profile
source ~/.bash_profile

Usage

0. Main program

usage: t2tools.py [-h] {centel,visual,gapcount} ...

options:
  -h, --help            show this help message and exit

sub commands:
  {centel,visual,gapcount}
    centel              Identify centromeres and telomeres
    visual              Visualizing trf data
    gapcount            Get gap counts

Notice: details of sub commands were described below.

1. Identify centromere and telomere for genome

a) Usage

usage: t2tools.py centel [-h] -f FASTA [-p] [-w WINDOW_SIZE] [-s STEP_SIZE] [--trf_options TRF_OPTIONS]
                         [--telo_type {plant,animal}] [--lower LOWER] [--upper UPPER] [--copy COPY] [--score SCORE] -o
                         OUTPUT [-t THREADS]

options:
  -h, --help            show this help message and exit
  -f FASTA, --fasta FASTA
                        fasta file or directory
  -p, --split           split fasta or not, only for single fasta file
  -w WINDOW_SIZE, --window_size WINDOW_SIZE
                        window size for splitting fasta, must be integer or scientific notation, like: 10000, 1e4
  -s STEP_SIZE, --step_size STEP_SIZE
                        step size for splitting fasta, must be integer or scientific notation, like: 10000, 1e4
  --trf_options TRF_OPTIONS
                        custom parameters for running trf:<match> <mismatch> <delta> <PM> <PI> <minscore> <MaxPeriod>
                        [options], default: 1 1 2 80 50 200 2000
  --telo_type {plant,animal}
                        pattern for telomere search, plant search TTTAGGG, animal search TTAGGG, default=plant
  --lower LOWER         lower size of centromere repeat monomer, default=50
  --upper UPPER         upper size of centromere repeat monomer, default=200
  --copy COPY           minium copy number of centromere repeat monomer, default=10
  --score SCORE         minium score of centromere repeat monomer, default=2000
  -o OUTPUT, --output OUTPUT
                        output directory
  -t THREADS, --threads THREADS
                        threads, default: 10

b) Example

t2tools.py centel -f chrom_dir -o wrkdir -t 24 --lower 50 --upper 250

c) Result

• trf_total.bed: a text file that contain several columns extracted from the dat file of trf like below

sid	start_pos	end_pos	length	copy_num	score	pattern	seq
Chr1	11	2711	2701	432.2	2306.0	ACCCTA	ACCCTAACCCTAACCCTAACCCTA...

• all_candidate_centro.list: a text file that contain all candidate centromere regions
• best_candidate_centro.list: a text file that contain best candidate centromere regions
• all_candidate_telo.list: a text file that contain all candidate telomere regions
• best_candidate_telo.list: a text file that contain best candidate telomere regions
• whole.pdf: a distribution plot of "Repeat monomer length (nt)" and "Number of monomer"
• separated.pdf: similar with whole.pdf but draw each chromosome separately

2. Visualize trf data

a) Usage

usage: t2tools.py visual [-h] -i INPUT [--lower LOWER] [--upper UPPER] -o OUTPUT

options:
  -h, --help            show this help message and exit
  -i INPUT, --input INPUT
                        input trf directory
  --lower LOWER         lower size of centromere repeat monomer, default=50
  --upper UPPER         upper size of centromere repeat monomer, default=200
  -o OUTPUT, --output OUTPUT
                        output directory

b) Example

t2tools.py visual -i trf_dat -o visual --lower 50 --upper 250

c) Result

• whole.pdf: a distribution plot of "Repeat monomer length (nt)" and "Number of monomer"
• separated.pdf: similar with whole.pdf but draw each chromosome separately

3. Get gap counts

a) Usage

usage: t2tools.py gapcount [-h] -f FASTA [-o OUTPUT]

options:
  -h, --help            show this help message and exit
  -f FASTA, --fasta FASTA
                        fasta file
  -o OUTPUT, --output OUTPUT
                        output statistic, if not set, output to stdout

b) Example

t2tools.py gapcount -f chrom.fa -o chrom.gap_cnt.txt

c) Result

A text file with two columns, first column is sequence id, second column is gap count, the last row is "Total" means total count of gaps