Commit fc2205bd authored by Matej Lexa's avatar Matej Lexa
Browse files

Update README.md

parent 3d62269e

README.md

+12 −12
Original line number Diff line number Diff line 
# nested



#### Introduction

## Introduction



*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*
@@ -10,7 +10,7 @@ in the input. Unlike other similar software, *TE-greedy-nester* is structure-bas 
de-novo retrotransposon identification software *LTR Finder*, relying on sequence information 

only secondarily.



#### External tools

## External tools

Program is using other external tools. Before usage make sure you have the following tools installed:



- LTR finder (v 1.05+) -
@@ -20,7 +20,7 @@ https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=Do 
- genometools (v 1.5.8) with gt sketch -

https://github.com/genometools/genometools



#### Installation - a step-by-step guide

## Installation - a step-by-step guide



```

chmod +x setup.sh
@@ -29,13 +29,13 @@ sudo ./setup.sh 


### Prerequisites



## ncbi blast+

#### ncbi blast+



```

sudo apt install blast2

```



## LTR_finder

#### LTR_finder



```

git clone https://github.com/xzhub/LTR_Finder.git
@@ -43,14 +43,14 @@ cd source 
make

```



## genome tools

#### genome tools



```

sudo apt-get install genometools

sudo apt-get install libgenometools0 libgenometools0-dev

```



## python requirements using pip3

#### python requirements using pip3



```

pip3 install bcbio-gff==0.6.4 click==6.7 decorator==4.2.1 networkx==2.1 numpy==1.14.2
@@ -59,22 +59,22 @@ PyYAML==3.12 six==1.11. --no-cache-dir 


### TE-greedy-nester



## clone whole directory from gitlab:

#### clone whole directory from gitlab:



```

git clone https://gitlab.fi.muni.cz/lexa/nested.git

cd nested

```



## modify respective paths in 'config_template.yml' save as 'config.yml' and call:

#### modify respective paths in 'config_template.yml' save as 'config.yml' and call:



```

sudo ./setup.sh

```



## that’s all!

#### that’s all!



#### Setting up the config

## Setting up the config

Before usage, **config.yml** needs to be set up:



- ltr finder paths - executable, prosite and tRNAdb
@@ -86,7 +86,7 @@ Before usage, **config.yml** needs to be set up: 


**Note**: `config.yml` is located by default in directory `/etc/nested/.`



#### Usage

## Usage

```

Usage: nested-nester [OPTIONS] INPUT_FASTA