Bedtools

Tool to edit and extract information from fasta files.

Installation

Get the latest version of the program from the source:

wget https://github.com/arq5x/bedtools2/releases/download/v2.29.1/bedtools-2.29.1.tar.gz

Decompress the file:

tar -zxvf bedtools-2.29.1.tar.gz

Go to the new folder:

cd bedtools2

Install:

make

In Linux you can install it using a package manager:

apt-get install bedtools

Bedtools have a lot of different utilities.

You can have a more detailed explanation on the flags, and the input files you need to execute these commands by typing:

bedtools <tool name>

The most straightforward and useful tools on a daily basis:

Extract a specific region of a fasta sequence according to coordinates (position) provided in a file in bed format:

bedtools getfasta -fi Source.fna -bed header_coordinate.bed -s -fo Selected_seq_region.fna

Bed file format for header_coordinate.bed in this case:

The file must have 4 columns:

header of the fasta sequences to be cut
start
end
name of the extracted sequence between start and end

The file should look like this:

chr1	5	10	myseq
chr2	12	28	myseq2