BBTools Table of Contents

Description

BBTools is a robust suite of fast tools for bioinformatics analysis. It is written in Java and usable on any operating system.

BBTools is developed at the Department of Energy's Joint Genome Institute and is distributed open-source, free for unlimited use by anyone. For more details see license.txt.

Additional documentation is in the bbmap/docs folder.

Installation

Extract the contents of BBMap_(version).tar.gz with:

tar -xzvf BBMap_(version).tar.gz

This extracts everything to a new directory named bbmap in the current directory.

For ease of use, add the shellscripts to your path, e.g.:

export PATH=$PATH:/path/to/bbmap/

Requirements

Requires Java 7 Runtime Environment or later (8+ is preferred). BBTools is developed and tested with Oracle's JDK 8, and in some cases memory allocation is slightly different under OpenJDK. BBTools can also benefit from samtools, sambamba, pigz, pbzip2, lbzip2, bzip2, and bgzip, though none are required. Specifically:

• .bam files can only be read or written if samtools or sambamba is in the path
• .bz2 files require pbzip2, lbzip2, or bzip2
• Block-gzipping (often used for vcf files) requires bgzip in the path
• Compression and decompression of .gz files is much faster with pigz in the path

Testing Installation

Check that BBTools is working with:

bbversion.sh

(returns version)

Test stats.sh on the PhiX reference included in the bbmap/resources folder:

stats.sh in=bbmap/resources/phix174_ill.ref.fa.gz

Expected output:

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
Main genome scaffold N/L90:             1/5.386 KB
Main genome contig N/L90:               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%

BBTools Scripts

Bash shell script wrappers are provided to make tools easier to run in Linux, though they are not strictly necessary. For example, the command:

reformat.sh in=x.fastq out=x.fasta

...could be executed on any operating system without using the script, like this:

java -Xmx1g -ea -cp /path/to/bbmap/current/ jgi.ReformatReads in=x.fastq out=y.fasta

This is a list of the shell scripts contained in BBTools with a brief description. Scripts not on this list are not intended to be used for analysis.

A detailed description and parameters for each tool are available by running the shell script with no parameters (e.g. bbcms.sh).

Tool Reference

Authors

• Brian Bushnell (bbushnell@lbl.gov)
• Bryce Foster (brycefoster@lbl.gov)
• Jon Rood
• Shijie Yao (syao@lbl.gov)

Citation

Please see bbmap/docs/citation.txt for information about citation.

Support

For questions and support:

• Email: bbushnell@lbl.gov
• Documentation: bbmap.org