Download BBTools from Sourceforge.
To install BBTools, download the latest version and extract the contents to your installation folder on the computer.
To run BBTools, you need to have Java 7 or higher installed on the computer.
For more information on the tools you can refer to the user guide in the bbmap/docs folder.
Linux/Macintosh
from the terminal window/linux shell:
$ cd (installation parent folder)
Extract the files using tar:
$ tar -xvzf BBMap_(version).tar.gz
this creates a subfolder named bbmap with the shell scripts and other necessary files.
To test the installation run stats.sh against the PhiX reference genome (included in the BBTools download):
$ (installation directory)/stats.sh in=(installation directory)/resources/phix174_ill.ref.fa.gz
A C G T N IUPAC Other GC GC_stdev
0.2399 0.2144 0.2326 0.3130 0.0000 0.0000 0.0000 0.4471 0.0000
Main genome scaffold total: 1
Main genome contig total: 1
Main genome scaffold sequence total: 0.005 MB
Main genome contig sequence total: 0.005 MB 0.000% gap
Main genome scaffold N/L50: 1/5.386 KB
Main genome contig N/L50: 1/5.386 KB
Max scaffold length: 5.386 KB
Max contig length: 5.386 KB
Number of scaffolds > 50 KB: 0
% main genome in scaffolds > 50 KB: 0.00%
Minimum Number Number Total Total Scaffold
Scaffold of of Scaffold Contig Contig
Length Scaffolds Contigs Length Length Coverage
-------- -------------- -------------- -------------- -------------- --------
All 1 1 5,386 5,386 100.00%
5 KB 1 1 5,386 5,386 100.00%
Microsoft Windows
Use a program to un-gzip and untar the BBMap_(version).tar.gz file such as 7-zip to an installation folder.
To test your installation from the Windows command prompt or PowerShell, run jgi.AssemblyStats2 against the PhiX reference genome (included in the BBTools download):
C:\> java -cp (installation folder)\current jgi.AssemblyStats2 in=(installation folder)\resources\phix174_ill.ref.fa.gz
A C G T N IUPAC Other GC GC_stdev
0.2399 0.2144 0.2326 0.3130 0.0000 0.0000 0.0000 0.4471 0.0000
Main genome scaffold total: 1
Main genome contig total: 1
Main genome scaffold sequence total: 0.005 MB
Main genome contig sequence total: 0.005 MB 0.000% gap
Main genome scaffold N/L50: 1/5.386 KB
Main genome contig N/L50: 1/5.386 KB
Max scaffold length: 5.386 KB
Max contig length: 5.386 KB
Number of scaffolds > 50 KB: 0
% main genome in scaffolds > 50 KB: 0.00%
Minimum Number Number Total Total Scaffold
Scaffold of of Scaffold Contig Contig
Length Scaffolds Contigs Length Length Coverage
-------- -------------- -------------- -------------- -------------- --------
All 1 1 5,386 5,386 100.00%
5 KB 1 1 5,386 5,386 100.00%