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add LTRfind info to readme
Jun 18, 2021
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LTRfind
LTRfind
 
 
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readme.md

LTRfind: a pipeline for get LTR and LAI ( base on LTR_retriever)

1. Install require software by conda

conda create -n LTR_retriever
conda activate LTR_retriever
conda install -y -c conda-forge perl perl-text-soundex
conda install -y -c bioconda cd-hit repeatmasker
git clone https://github.com/oushujun/LTR_retriever.git
./LTR_retriever/LTR_retriever -h
conda install -c bioconda seqkit
chmod 757 LTRfind
./LTRfind -h

you also can add the path of LTRfind to the ~/.bashrc.

2.how to use it

It is mainly used for the identification of diploid and polyploid LTR and the calculation of LAI value.

Purpose:

Get the LTR_RTs in the genome and calculate the LAI value of the genome at the same time. for Diploid use (-D|Diploid) for Polyploid (up to octoploid) use (-P|Polyploid)

Usage:

	-h|--help 
	-D|Diploid Species genome.fa 
	-D|Diploid Species genome.fa ChrString 
	-P|Polyploid -abbr Species -g genome.fa -chr ChrString -p1 Ghir_A -p2 Ghir_D 
	-P|Polyploid -abbr Species -g genome.fa -p1 Ghir_A -p2 Ghir_D 
	-V | --version

Example:

	LTRfind -D A.thaliana /path/A.thaliana.fa 
	LTRfind Diploid A.thaliana /path/A.thaliana.fa chr
	LTRfind -P -abbr Species -g genome.fa -chr ChrString -p1 Ghir_A -p2 Ghir_D 
	LTRfind -P -abbr Species -g genome.fa -chr ChrString -p1 Ghir_A -p2 Ghir_D -p3 Ghir_C 
	LTRfind -P -abbr Species -g genome.fa -chr ChrString -p1 Ghir_A -p2 Ghir_D -p3 Ghir_C -p4 Ghir_B
	LTRfind Polyploid -abbr Species -g genome.fa -p1 Ghir_A -p2 Ghir_D

Note:

In run -D|Diploid ，if you input the ChrString , will extract the Chromosome sequence for LTR and LAI (not analysis the scaffold sequence). Input genome file must be .fa,not support .fa.gz. the genome.fa sequence ID should be less then 15 character. if your file is report over 15 character, can use seqkit seq -i genome.fa >new.genome.fa to extract the ID and delete the info after the ID if your input genome.fa ChrID may be like >1,in this case, you cannot use the ChrStr field to extract chromosome data and filter scaffold. It is recommended to use LTRfind after filtering by yourself. The ID length of genome.fa cannot exceed 15 characters.

3. Input

Diploid:

  • speciesname
  • genome.fa
  • ChrStr (can be omitted)

Polyploid:

  • speciesname
  • genome.fa
  • ChrStr (If you do not provide this parameter, it is assumed that the genome file you provide only contains the sequence of the chromosome.)
  • p1
  • p2
  • p3
  • p4

Example:

Polyploid:

for Ghirsutum.fasta head Ghirsutum.fasta

>Ghir_A01
TAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAA
ACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACC
CTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTA
AACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAAC
CCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAAACCCTAAACCCTAAACCC
TAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAA
ACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACC
CTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTA
AACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAAC
...
>Ghir_D01
AAACCCTAAACCCTAAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAAACCCTAAACCCTAAACCCTAAACCCTA
AACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAAC
CCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCT
AAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAA
CCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCC

should be run like this: LTRfind -P -abbr G.hirsutum -g Ghirsutum.fasta -chr Ghir_ -p1 Ghir_A -p2 Ghir_D

Diploid

head Arabidopsis_thaliana.fa

>chr01 dna:chromosome chromosome:TAIR10:1:1:30427671:1 REF
CCCTAAACCCTAAACCCTAAACCCTAAACCTCTGAATCCTTAATCCCTAAATCCCTAAAT
CTTTAAATCCTACATCCATGAATCCCTAAATACCTAATTCCCTAAACCCGAAACCGGTTT
CTCTGGTTGAAAATCATTGTGTATATAATGATAATTTTATCGTTTTTATGTAATTGCTTA
TTGTTGTGTGTAGATTTTTTAAAAATATCATTTGAGGTCAATACAAATCCTATTTCTTGT
GGTTTTCTTTCCTTCACTTAGCTATGGATGGTTTATCTTCATTTGTTATATTGGATACAA

bash LTRfind -D A.thaliana Arabidopsis_thaliana.faor bash LTRfind -D A.thaliana Arabidopsis_thaliana.fa chr

4. Output

All the output is the same with LTR_retriever. For Chinese, there are detail info links in Chinese.

5. Author & Version

  • Build date:2021.06.17
  • Last update: 2021.06.18
  • Version: 0.02
  • Author: Mol Chai
  • Email: chaimol@163.com