Skip to content

Latest commit

 

History

History

38.99

Folders and files

NameName
Last commit message
Last commit date

parent directory

..
 
 
 
 

BBTools

This image implements Brian Bushnell's BBTools.

Includes

In addition to the BBTools, this container also provides the following pieces of software to enhance the BBTools:

To see all of the executables in this image, run the following command inside a container:

ls /usr/local/bin

Documentation is in the /opt/bbmap/docs/ directory, and in each tool's shell script in /opt/bbmap/.

Example Usage

(adapted from /opt/bbmap/pipelines/covid/processCorona.sh)

Interleave a pair of FASTQ files for downstream processing:

reformat.sh \
    in1=${SAMPLE}_R1.fastq.gz \
    in2=${SAMPLE}_R2.fastq.gz \
    out=${SAMPLE}.fastq.gz

Split into SARS-CoV-2 and non-SARS-CoV-2 reads:

bbduk.sh ow -Xmx1g \
    in=${SAMPLE}.fq.gz \
    ref=REFERENCE.fasta \
    outm=${SAMPLE}_viral.fq.gz \
    outu=${SAMPLE}_nonviral.fq.gz \
    k=25